A phylogeny of the frog genus Vibrissaphora and seven Leptobrachium species was reconstructed based on 3808 base pairs of mitochondrial and nuclear DNA sequence data. Maximum parsimony, Bayesian, and statistical parsimony approaches were employed to reveal the historical relationships among the recovered haplotypes. The species of the genera Vibrissaphora and Leptobrachium failed to form their respective monophyletic groups. Therefore, Vibrissaphora should be part of the genus Leptobrachium. Our analysis also further delineated several species boundaries; Leptobrachium chapense is not a single species, rather, a species complex. On the other hand, although L. liui demonstrated substantial morphological variation, all populations belong to one species. The RAG-1 data revealed a case of species-level non-monophyly; when studying slowly evolving genes, population coalescence may not have been reached within species. The phylogenetic comparative analysis revealed a positive correlation between evolution of male nuptial spines and reversed sexual size dimorphism in this group. Resource defense polygyny and male parental care are possible explanations for the presence of large male size.