There are few reports of cloacal mycobiota on wild reptiles, and in particular, fungal presence and functionin Caiman latirostris remains unknown. Our objective was to describe the fungal community present in the cloaca ofwild female broad-snouted caimans during their reproductive season determine whether the number of fungi has somerelationship with the female’s corporeal condition. Fungi were found in 9 out of 13 cloacal samples and 14 species offungi were isolated and identified. Three of the species isolated had the highest occurrence values, and 2 of them arepathogenic. In this case, body condition index had no relationship with fungal frequency; the fungi found in this studymay have originated from soil habitat and nest substrate that are in constant contact with the cloaca of the C. latirostrisfemales. The findings in this work support the theory that reptiles are facultative carriers of fungi or their spores.