Animal Information

Is There Fungus Among us? Turtle and Tortoise Fungal Infection Or Shell Rot

Is there Fungus among us? It is estimated that 3 percent of US and European households harbor non-typical companion animals. These captive animals are prone to several infectious diseases, including superficial as well as deep and systemic diseases.

The superficial fungus does not pose a long-term health issue but is remedied easily.

Dermal bone is a characteristic feature of chelonian species, it is present in the carapace, plastron and lateral struts connecting these structures and does not match the pattern of overlying keratinized scutes. Turtles and tortoises might suffer from fungal infection involving the skin, scale armor, and carapace.

Excessively high humidity, low environmental temperature, concurrent disease, malnutrition, and other stressors may predispose reptiles to development of various mycoses. Little is known about the pathogenesis of systemic mycoses, which can develop over a long period, but maintaining good sanitation and husbandry reduces the frequency of infection.

The longer an infection of this type persists untreated, the greater the danger of it turning into a much more serious systemic infection or ulcerating abscess, deep in the bony tissue. Veterinary attention should be sought in all cases. Common symptoms may include:-

  • Unpleasant discharge or smell from the affected area;
  • Fluid, often reddish, visible under the plates of the shell;
  • Softening or lifting of the shell plates;
  • Soft areas or pitting appearing in or just under the surface of the shell;
  • Shell plates falling off, leaving live or necrotic bony tissue exposed.

Spotting A Fungus On Your Turtle…

Aquatic turtles can develop fungus if they are kept in a poorly maintained aquarium environment. The first signs of a fungal infection are small patches, usually on the shell but occasionally on the legs or neck. These are green in color and should not be confused with the white patches which are the first sign of a shed on the skin or shell. These shedding patches are quite distinctive, they are clearly a layer of the shell loosening from the lower one.

two brown sea turtle on tree branch
Photo by Samar Patil on

Fungal infections of turtles are very common and are usually caused by poor sanitation in the turtle’s tank. It is incredibly difficult to keep a turtle’s environment clean because of their habit of taking their food into the water to eat it and then subsequently defecating in the water as well.

This makes for a very slimy, smelly substrate which is absolutely perfect for the development of fungus. Add to that the fact that the tank is always nice and humid and warm and really the only surprising thing is that every turtle does not have a rampaging fungal infection all the time.

If turtles from humid environments are allowed to over-dry, shell and skin condition will rapidly deteriorate. If animals from arid environments are kept on damp substrates, the outer keratin may become soft and distorted and may permit pathogens to gain access. It is very important to keep all tortoises on an appropriate substrate and to also keep it clean.

Spotting A Fungus On Your Tortoise…

Sulcatas and other desert tortoises that are kept on too wet of a substrate can develop bacterial or fungal infections of the plastron and skin. Shell-rot is a generic term which describes diseases of a tortoise’s shell. These diseases often follow damage or abrasions, even those that are seemingly minor in extent.

Strangely enough, ticks can attach themselves to tortoises very easily, and will provide that essential penetrative injury shell-rot pathogens need to establish themselves.

In fact, any penetrative damage to the shell may result in unwelcome bacteria, or other pathogens gaining access to the blood-rich living tissue present just below the outer, hard, layer of keratin.

Is Shell Rot Contagious?

Shell rot depending on the type can be highly contagious, and one infected animal can spread it rapidly to all others it comes into contact with. It is not a condition that should be ignored or underestimated.

Seek professional advice at an early stage if you believe you have an affected tortoise or turtle. In the long term, untreated diseases of this nature are killers, but given appropriate treatment at an early stage, a complete recovery is usually assured.

Treatment of fungal infections…

As long as the turtle or tortoise is otherwise well and you have definitely identified the patches as fungus, getting rid of them is relatively easy. The environment will need to be cleaned out thoroughly before returning the turtle or tortoise to it, so it is a good idea to prepare alternative quarters for the animal to stay in before getting to work on eradicating the fungus from the skin and shell. Also, all other companion turtles will need to be treated, although it is unlikely in any event that only one is affected.

The first part of the treatment is to clean the animal off, using a very soft toothbrush and some hypoallergenic soap, we use Dawn dish soap, anything fragrance-free will do. Don’t use too much, just enough to soften and remove the main growths of the fungus. Then the turtle or tortoise should be rinsed and dried off completely. If it doesn’t like being handled, put it in the clean habitat under a lamp to dry off, then wipe it all over with a very dilute solution of iodine. Your vet will be able to recommend a suitable brand.

Don’t dry the turtle or tortoise off with a towel this time, but put it back to dry under a lamp. Alternate this treatment with a salt bath, again allowing the solution to dry on the shell. Fungi hate salt and so this will both kill the old fungus and inhibit the growth of new. Both of these treatments should ideally be continued for at least a fortnight.

Cleaning the tank and keeping it clean.

While the turtle is enjoying its spa treatment, clean out the tank thoroughly by emptying it out completely and scrubbing the glass until it is totally clean. Make sure that you brush in all the corners. Clean off or replace any moveable features like basking platforms and allow it all to dry off before replacing the water and returning the turtles.

Water filters designed for fish tanks don’t cope too well with turtle environments as turtles are much dirtier feeders and pooers than fish and the filter is not often up to the task. Once you have got rid of all the fungi and molds in the tank, a good plan is to replace half of the water once a week.

This way any beneficial bacteria stay present, but the much of the gunk is removed. Try and keep on top of fragments of food in the water and keep the glass as clean as possible.

A basking lamp is vital for the general health of the turtle, as it needs to get dry once in a while as well as being warm. If the animal is always wet, cold, and dirty it will not only almost certainly fall victim to more fungal infections but it will also be very likely to develop much more serious conditions such as shell rot and respiratory tract infections.

IsThere A Difference Between Rot and Fungus?

A fungus is quite distinct from shell rot, There is a parting of the layers of the shell. In shell rot, though, it usually starts at an injury site and goes much deeper than one layer. Rot also looks unhealthy and may have fluid under the lifted layer and there is almost always an unpleasant smell. Fungal growths look like small raised greenish patches and can grow quite quickly.

Some common causes of shell-rot include:

Aggression by other tortoises: Some males are especially aggressive and will repeatedly “beat up” other males or females. At the typical main impact site, just above the tail, instances of shell rot are especially common. Mixing incompatible species is one sure way to initiate the problem.

Poor vivarium hygiene: Dirty substrates will harbor innumerable pathogens. One small injury and serious consequences may well follow.

Incorrect substrate humidity: If turtles from humid environments are allowed to over-dry, shell and skin condition will rapidly deteriorate. If animals from arid environments are kept on damp substrates, the outer keratin may become soft and distorted and may permit pathogens to gain access.

Ticks: Ticks can attach themselves to tortoises very easily, and will provide that essential penetrative injury shell-rot pathogens need to establish themselves..

In aquatic species, water hygiene: Good filtration is essential. If a turtle injuries its shell in filthy water, shell disease often follows. Use of a UV-C sterilizer in the filtration circuit can substantially reduce the danger of shell and skin infections. Soft-shell turtles are especially susceptible to problems of this nature.


Infection of the bone, called “osteomyelitis,” is very serious and painful, and it requires aggressive treatment. In severe osteomyelitis cases, animals may have loose or missing teeth. Snakes may develop ocular infections if the infection travels into space between their eyes and spectacles. Pneumonia may result from the chronic weakness and if the reptile inhales organisms into its windpipe and then down into its lungs.

photo of snake
Photo by Jan Kopřiva

The causes of infectious stomatitis are many, but the underlying common denominator is usually related to stress, which causes the immune system to function improperly.

When this happens, the reptile becomes susceptible to many different disease-causing organisms. These organisms, most frequently bacteria but viruses or fungi in some cases, can begin reproducing unchecked, resulting in a serious infection.

In some cases, tumors appear in the tissues surrounding the mouth. If a tumor ulcerates, it may look like infectious stomatitis. For this reason, it is always important for a veterinarian to biopsy the affected tissues in order to procure a diagnosis, especially in cases where ordinary treatment does not resolve the clinical signs.

Treatment depends on which organisms are involved with the disease and the severity of the infection. Oral cleaning with specific medications may be necessary, but it is important to avoid additional tissue damage by overzealous cleaning of affected tissues. If systemic antibiotics or antifungal agents are needed, either injections or oral medications may be administered.


Dermatophytosis has been described in all orders of reptiles. GeotrichumFusarium, and Trichosporonare the genera most frequently isolated. In most cases, cutaneous injury precedes a secondary fungal infection.

Chelonians with fungal infections of the shell can be treated by local debridement and topical application of Lugol solution or povidone-iodine. Exposure to ultraviolet light also may be beneficial.

ball ball shaped blur color
Photo by Pixabay

Ulceration of GI tissues has been associated with infections by Mucor and Fusarium spp. Chronic visceral granulomatous disease of liver, kidneys, and spleen has been caused by Metarhizium and Paecilomyces spp. Few signs other than weight loss are seen before death. Animals may continue to feed until a few days before death.

The most frequent sites of mycotic infection are the skin and respiratory tract. MetarhiziumMucor, and Paecilomyces spp are frequent isolates. Aspergillus and Candida spp have been isolated from pulmonary lesions of lizards and chelonians. Most infections involve granuloma or plaque formation with resultant signs of respiratory distress before death.

Dematiaceous Fungi

glass blur bubble health
Photo by Edward Jenner

Dematiaceous fungi can frequently be discerned in tissue specimens stained with conventional hematoxylin and eosin; they appear as septate, brownish hyphae or yeast-like cells, reflecting their high melanin content.

Masson-Fontana staining for melanin confirms their presence. Phaeohyphomycosis is distinguished from chromoblastomycosis and mycetoma by the absence of specific histopathologic findings such as sclerotic bodies or grains in tissue.

Mouth Rot

  • Nutritional secondary hyperparathyroidism. This common problem in reptiles may result in a misshapen jaw. Lips are pulled over misshapen bones, and as a result gum tissue develops exposure gingivitis. This syndrome superficially looks like infectious stomatitis, and it will eventually turn into the infection if it is not treated early and properly.
  • Mites. Although not a direct cause, mites can contribute to the development of the infection because they can transmit infectious organisms associated with the disease, such as Aeromonas and Pseudomonas bacteria, when they bite and suck blood.
  • Trauma. Rostral abrasions from a reptile constantly rubbing its nose on a surface, such as a screen top or glass enclosure, can result in abrasions that allow opportunistic bacteria to enter the tissues and cause infection.

More Turtle And Tortoise Diseases…

Necrotic stomatitis is an infection often caused by either the bacteria Pseudomonas or Aeromonas. It is commonly known as ‘mouth rot’ and is a common bacterial infection in turtles and tortoises. Mild conditions are often treated by swabbing the infected areas with diluted Betadine. More established infections often respond to antibiotics including cephalosporins and amoxicillin.

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In severe cases, injectable antibiotics must also be used. There are several factors that predispose turtles and tortoises to develop mouth rot. The most common is poor jaw alignment often caused by overgrown, damaged, or improperly trimmed beaks. Mouth injuries from thorns contacted during feeding can also be a cause. Tortoises may be particularly susceptible to these infections during hibernation.

Eye infections and conjunctivitis often begin as a small white spot on the surface of the cornea (the clear front portion of the eye). As the infection progresses, it can spread over the entire surface and create an ulcer on the eye.

It is important that these infections are not confused with cataracts or the less common hypovitaminosis A (Vitamin A deficiency). Infections may also occur in the eyelids creating irritation and swelling. The cause of many of these infections is contaminated water in aquatic or semi-aquatic turtles or low humidity in tortoises.

The treatment of eye infections usually consists of topical antibiotic eye drops with neomycin, chloramphenicol, or gentamycin most commonly used. In aquatic turtles, injectable antibiotics may often have to be used due to the inability of keeping topical drops or ointments on the eye for a long enough time to provide treatment.

Cloacitis is a bacterial infection of the cloaca that results in an inflamed cloacal opening and a foul-smelling discharge. These infections are often associated with parasitic infections, or a stone-like cloacal calculus (mineral deposit).

Treatment consists of removing the stone, treating the parasitic infection, if present, and then irrigating the cloacal area with a dilute Betadine or chlorhexidine solution. A topical antibiotic ointment is then applied to the cloacal opening.

Pneumonia occurs in one of two forms. The first is the acute type and can appear suddenly and cause death in just a matter of hours, if not treated quickly. The turtle will have problems breathing, such as respiratory distress with gasping and open mouth breathing. There may be coughing or disorientation. Some tortoises with acute pneumonia may actually become hyperactive.

The second form is chronic, and turtles may also have problems breathing and chronic nasal discharge. Radiographs (x-rays) may help confirm a tentative diagnosis. Treatment for both forms consists of injectable antibiotics. The acute form usually responds better to treatment. Common antibiotics include enrofloxacin (Baytril), ciprofloxacin, oxytetracycline, or ampicillin (may cause swelling at the injection site).

Ulcerative Shell Disease is often called SCUD or ‘shell rot’ and comes in two primary forms. The dry form is often associated with a fungal infection and needs to be treated with antifungal medications. The wet form is associated with gram-negative bacteria and often develops after an injury to the shell. Treatment consists of removing the infected scute and irrigating the area with a diluted Betadine solution. A topical antibiotic is then often applied.

Septic Arthritis and Articular Gout are both serious conditions that can be seen individually but are often found together in the same affected joint. The signs include swelling of the limb joints, stiffness, and pain when the joint is manipulated. This condition is sometimes confused with rickets caused by a Vitamin D deficiency.

Ear Abscesses are a relatively common problem, particularly in American Box Tortoises. The common signs are swelling of the tympanic membrane and the resulting discharge of pus into the back of the throat via the eustachian tube. Since these infections can often be very advanced before they are noticed, treatment usually consists of surgically opening and draining the abscess. In the early stages of the infection oral or injectable antibiotics can be used. These infections are often associated with contaminated water or improper temperature and humidity levels.

Abscesses are very common in all reptiles including turtles and tortoises. The most common locations are the ears, legs, nasal passageways, jaw, and liver. Abscesses often present as hard lumps or swellings under the skin. Antibiotics are not usually very effective in controlling these abscesses, so surgical removal is the preferred method of treatment.

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  1. hello…how often do you wash them in Dawn and put the vaseline on there? do you use any other kind of topical solution to stop the fungus? what about antibiotics?

    1. Hi Susan, We bath them with the Dawn and Vaseline only once or twice per year. We have tried lots of other products such as olive and coconut oil. All works. But must be reapplied often. We found the petroleum based jelly to be truly effective and long term. It really takes just a small amount. Less than you put on your toothbrush. Using a toothbrush makes it easy too. I would think there is a place for antibiotics when it comes to severe shell rot. Because most turtles can recover from this damage easy. If there is an odor to the fungus, I would guard and ask a vet. Here is a link to a video we just published where we bathed and fed a new tortoise named Daisy. Please check it out.

    1. I am sorry to hear that your tort is having issues. The Russian can have this as they are from a dry environment. I think it will be just fine with treatment.

      Antibiotic cover is essentially in severe shell rot cases or if the shell has been fractured. Topical antibiotics such as silver sulfazadine cream applied daily can be enough for many cases.

      If kept clean the keratin will regrow and you will never know it happened.

      Thank you for finding our page.

  2. Hello, I have a small box turtle that was in the wild and has been with us about 30 years. Recently his face started turning white. Not his shell, just both sides of his head starting at the mouth going about a quarter of the way up his head. Otherwise he seems very happy. I don’t know how to treat it.

  3. What do you do about thrush in the mouth after having to provide antibiotics longer term?

Let us know your ideas and comments below!

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