Few studies have explored the ecology and interrelationship with other organisms of the many endangered freshwater turtle species inhabiting the Neotropical Region. The focus of the current study was to shed light on the relationship between Neotropical turtle carapaces and primary producers, insofar as the surface of former constitutes a suitable substrate for the colonization and establishment of the latter. The under-explored relationship between turtle carapaces and the diatom assemblages inhabiting them was investigated and characterized in terms of taxonomic and biological traits (bio-volume, life-form, and attachment). The carapaces of seven native turtle species were surveyed. Among these carapaces, a total of 45 diatom taxa were found, and diatom taxa varied among turtle species. Podocnemis vogli and Podocnemis expansa supported more diverse diatom assemblages than Podocnemis lewyana, Rhinoclemmys diademata, and Rhinoclemmys melanosterna, which were dominated by Navicula spp. Analysis further showed that carapace size did not explain differences in diatom diversity. However, a trait-based analysis suggests that both carapace roughness and an assemblage’s successional stage might explain the differences in assemblage composition. Because turtles can serve as dispersal vectors, characterizing their epibiont diatom assemblages may contribute to our understanding of diatom distribution on larger scales, as well as, give us some clues as to the auto-ecology of turtles that help us to effectively determine conservation areas for these endangered species.