Taxonomy and species boundaries within the Rhacophorus rhodopus and Rhacophorus bipunctatus complexes are very confusing. In this study, we attempt to delimit the species boundaries and test the currently accepted taxonomic assignments within these two complexes based on newly collected samples and previously published data across their distributions. Phylogenetic analyses revealed that the R. rhodopus and R. bipunctatus complexes consisted of six distinct clades (labeled A‒F) that diverged from each other by genetic distances (p-distance) ranging from 5.3% to 9.2% in 16S rRNA sequences, and accordingly analyses of species delimitation placed them into six species, of which three correspond to known species (R. rhodopus, R. bipunctatus, and R. napoensis) and three represent different cryptic species. Rhacophorus rhodopus (Clade C) is distributed in southern Yunnan, China, northern Laos, and northern and central Thailand; R. bipunctatus (Clade F) is distributed in northeastern India and western and northern Myanmar; and R. napoensis (Clade B) is distributed in Guangxi, China and northern Vietnam. Based on both molecular and morphological evidence, we described the clade consisting of samples from Hainan, China and central Vietnam (Clade A) as a new species, Rhacophorus qiongica sp. nov. There are two cryptic species requiring additional morphological studies: one only contains samples from Motuo, Xizang, China (Clade E), and the other is distributed in western Yunnan, China, central Myanmar, central Thailand, and Malaysia (Clade D). Additionally, our results supported the idea that some old GenBank sequences of R. reinwardtii need to be updated with the correct species name.