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. Aspergillus, Candida, Cladosporium, Metarhizium, Mucor, Paecilomyces, Penicillium spp, and the Chrysosporium anamorph of Nannizziopsis vriesii are a few of the organisms associated with systemic disease. Reports of successful treatment of systemic mycoses in reptiles are few. Suggested treatments for deep fungal respiratory infections include amphotericin B, itraconazole, fluconazole, and voriconazole. For superficial or localized mycotic infections, surgical removal of the granuloma with local wound treatment is advised. Basidiobolus spp, pathogenic for mammals, are found in feces of healthy reptiles.

Dermatophytosis has been described in all orders of reptiles. Geotrichum, Fusarium, and Trichosporon are 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.

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. Metarhizium, Mucor, 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. Candidiasis in large snakes has been treated with nystatin (100,000 U, PO, for 10 days).