To determine the potential for intra-oviductal contamination of sea turtle eggs with fungi accumulated during nesting, turtles were sampled for clocal fungi. Pre-gravid females had a low incidence (17%) of clocal fungi (Acremonium, Cladosporium, Penicillium). A higher occurrence (30%) of these same fungi in courting animals, that had not bred for >2 years, was probably the result of transfer during intromission. Nesting (75%) and inter-nesting (100%) turtles had the greatest occurrence and diversity of clocal fungi (Acremonium, Aspergillus, Chrysoporium, Fusarium, Mucor, Penicillium, Phialophora, Sporothrix, Stachybotrys). The incidence of clocal fungi rapidly decreased after nesting, to 28% within one year (Acremonium, Penicillium) and 13% in animals that bred at least two years earlier (Acremonium, Cladosporium Penicillium). The other species of fungi are probably lost during defaecation. If fungal spores can be transported and maintained in the sea turtle oviduct by the same mechanisms as for spermatozoa, acute intra-seasonal contamination of eggs by fungi may be possible. The potential for chronic inter-seasonal contamination of the oviduct appears to be low.