Hotspots of amphibian species diversity typically occur in limited geographical ranges, and critically endangered habitats often contain a large number of endemic amphibian species. In such regions, it is prudent to engage conservation strategies for multiple amphibian species simultaneously. To correctly identify suitable habitats for multiple species, species interactions should be considered in species distribution models. In this study, we adopted a joint species distribution model to determine the abiotic and biotic factors that affect calling-site choice in three endangered co-occurring frog species on Amami-Oshima Island, and examined whether they co-occur more than expected after considering the overlapping preferences in environmental variables. Occurrences of Babina subaspera, Odorrana splendida, and O. amamiensis were assessed by monitoring mating calls using automatic digital voice recorders at 67 sites in 12 streams and explained by 8 environmental variables: water flow volume, temperature, pH, electrical conductivity, ammonium (NH₄ -N) concentration, elevation, slope, and forest stand age. The flow volume was negatively associated with occurrences in B. subaspera and O. splendida, but not O. amamiensis. Odorrana splendida occurred more frequently at higher elevations. Babina subaspera and O. splendida showed positive environmental correlations, indicating that they preferred similar environmental conditions, while exhibiting no negative relationships with each other. Our results indicated that B. subaspera and O. splendida do not avoid each other despite potential competition during the tadpole stage. Our results demonstrated that conserving preferable areas for O. splendida would also benefit B. subaspera with no negative species interactions, but not O. amamiensis. Considering species interactions in species distribution models will help us take more effective measures in the conservation of multiple species.