The loggerhead sea turtle (Caretta caretta) is a keystone species with an important ecological role in marine ecosystems. They are the most widespread sea turtles in the Mediterranean Sea, and there are ongoing conservation efforts aimed at preventing their population decline. These efforts can be helped through loggerhead-associated microbiota studies by facilitating the diagnosis and treatment of illnesses caused by pathogenic microorganisms. Despite that, such studies are scarce, and comprehensive studies of fungal communities associated with loggerheads are non-existent. The aim of this study was to describe the structure and composition of endobiotic and epibiotic mycobiota of Mediterranean loggerheads. Microbial fungi were explored from the turtles’ cloacal and tank water samples by analysing sequences of the ITS2 region of rDNA and carapace and skin samples by analysing the V4 region of 18S rDNA. Cloacal and tank water mycobiota significantly differed, but the cloacal mycobiota did not show significant alteration in relation to the turtles’ age or hospitalisation length. Carapace and skin mycobiota were composed of the same dominant divisions, but in different proportions. Comparison of endo-, epi- and environmental mycobiota revealed marked differences in community composition. This study offers first insights into fungal microbial communities associated with loggerheads, providing the basis for future research