Social interactions of conspecifics are a function of complex relationships involving resource defense, antipredatory tactics, and mate acquisition. Consequently, individuals often associate non-randomly with conspecifics in their habitats, with spatial distributions of adults ranging from territorial spacing to aggregations. Site tenacity and cohabitation patterns have been well studied in many species of terrestrial salamander; however, less is understood about these behaviors in aquatic species. We examined the cohabitation patterns of intrasexual and intersexual pairs of the federally threatened, paedomorphic San Marcos salamander (Eurycea nana) under artificial shelters in a laboratory setting over a 20-day period. We found that intrasexual female pairs and intersexual pairs were found cohabiting more often than intrasexual male pairs. We also assessed site tenacity by examining shelter affinity and found that both males and females inhabited one of the two shelters more often than expected from random habitation, regardless of whether they were in intersexual or intrasexual pairings. Our results indicate that although both sexes of Eurycea nana exhibit site affinity, the sex of individuals is an important determinant of cohabitation patterns.