We investigated species composition, diversity, and seasonal variation of bat assemblages in the uplifted coral reef tropical forest of Taiwan. We mistnetted 584 bats of 10 species, accounting for one-third of the bat fauna of this island. Miniopterus schreibersii, Hipposideros terasensis, Rhinolophus formosae, and Murina puta were the most frequently caught and abundant species, together accounting for 79% of the relative frequency and 84% of the relative abundance; followed by Rhinolophus monoceros and Myotis taiwanensis. We found no evidence of the presence of Myotis muricola, but added Eptesicus serotinus, Myotis watasei, and Pipistrellus abramus to the list of species recorded from these forests. Both the total and mean numbers of species caught peaked in May–June, whereas the mean capture rates climaxed in July–August. Most species were captured year-round, but M. puta was more abundant in winter and M. taiwanensis was absent during late summer–early winter. The numbers of species present at interior and edge sites were similar, as were species composition and evenness and heterogeneity values. However, capture rates were 2-fold higher at interior than edge sites, in particular for H. terasensis, R. monoceros, and M. taiwanensis and were female-skewed, particularly for M. schreibersii and R. monoceros. The overall similarity in species composition between the forest interior and edge sites, based on assessments of bat captures or bat passes, was nearly 10% higher than the similarity between data of bat captures and bat passes within the forest interior and edge sites, respectively.