Gut microbiota of vertebrate hosts play crucial roles for the host they inhabit. In this study, we compared the composition and predicted functions of gut microbiota of female individuals belonging to four frog species from different habitats using bacterial 16S rRNA gene sequencing. Our results showed that the gut microbiota of the examined frog species were dominated by the phyla Firmicutes, Proteobacteria, Bacteriodetes, Verrucomicrobia, and Fusobacteria. There were significant differences in the relative abundance of dominant phyla among the four species, although the relative abundance of dominant phyla in the microbiota of individuals of Odorrana tormota was more evenly balanced (ranged from 10.45% for Fusobacteria to 27.21% for Bacteroidetes). The alpha diversity patterns varied depending on the microbial taxon level. At the phylum level, the Chao1 diversity was positively associated with body weight, with the diversity index scores of O. tormota and Amolops wuyiensis markedly lower than those of Odorrana schmackeri and Polypedates megacephalus. At the genus level, Chao1 diversity was associated with evolutionary relationships among species, with the Chao1 diversity index score for P. megacephalus of distant evolutionary relationships being significantly higher than the scores for frogs with close evolutionary relationships. Moreover, permutational multivariate analysis of variance revealed significant differences in the gut bacterial community structure among species (R² = 0.510, P = 0.001). Further, the predicted functions of the gut microbiota were similar for species with close evolutionary relationships but differed with distant evolutionary relationships. Taken together, our results indicate that wild frogs have species-specific microbial communities and provide insight into the ecological and evolutionary dynamics of host–microbe interactions.