Fungal infections affecting the integumentary system, the upper and lower respiratory system and the gastro-intestinal tract have been reported in many species of captive reptiles. Systemic mycoses are diagnosed rarely in reptiles, and in most cases, they are a postmortem finding. Commonly, immunocompromised reptiles, kept in suboptimal environmental conditions are affected. In many cases, mixed bacterial and fungal infections of opportunistic organisms may be present. A diagnosis of a primary fungal infection is based on proper selection and collection of diagnostic specimens such as biopsies of infected tissues. Treatment of fungal infections in reptiles includes administration of effective antifungal agents and correction of inappropriate environmental conditions such as poor hygiene, too high or too low temperature and humidity, inadequate diet, and stress from overcrowding. Few studies have investigated effective dosages and dosage intervals of antifungal agents in reptiles.