Sea turtles host a diverse array of epibionts, yet it is not well understood what factors influence epibiont community composition. To test whether epibiont communities of sea turtles are influenced by the hosts’ nesting or foraging habitats, we characterized the epibiota of leatherback, olive ridley and green turtles nesting at a single location on the Pacific coast of Costa Rica. We also compared the epibiota of these turtles to conspecific populations nesting elsewhere in the East Pacific. If epibiont communities are influenced by nesting habitats, we predicted that sympatrically nesting turtles would have comparable epibiont taxa. Alternatively, if epibiont communities are influenced by foraging habitats, we predicted the diversity of epibiont taxa should reflect the type and diversity of the hosts’ foraging habitats. We identified 18 epibiont taxa from 18 leatherback, 19 olive ridley and six green turtles. Epibiont diversity was low on leatherbacks (four taxa), but higher for olive ridley and green turtles (12 and nine epibiont taxa respectively). The epibiont communities of olive ridley and green turtles were not statistically different, but both were different from leatherbacks. In addition, conspecific sea turtles from other nesting locations hosted more similar epibiont communities than sympatrically nesting, non-conspecifics. We conclude that epibiont diversity of nesting sea turtles is partially linked to the diversity of their foraging habitats. We also conclude that the surface properties of the skin and carapace of these turtles may contribute to the uniqueness of leatherback turtle epibiont communities and the similarities between olive ridley and green turtle epibiont communities.