Sex‐biased dispersal, which influences species’ social organization, genetic structure and evolution, is an important life‐history event. Although sex‐biased dispersal in mammals and birds has been thoroughly studied, little is known about it in amphibians. In this study, we used eight highly polymorphic microsatellite loci and two mitochondrial DNA (mtDNA) genes to infer patterns of dispersal of the Omei tree frog (Rhacophorus omeimontis). We found that the comparison between two types of markers showed higher FST values in mtDNA compared to microsatellites. Consistently, comparison of pairwise and overall FST values between the sexes revealed higher differentiation in females than in males. Furthermore, the inbreeding coefficient (FIS) and population gene diversity (HS) were lower in females than in males, whereas relatedness (r) was higher in females than in males. Females exhibited relatively higher correlation between genetic distance and geographical distance than males. Additionally, the mean assignment index (mAIC) was lower in males, whereas the variance of assignment index (vAIC) was higher in males. These evidences reflect higher genetic differentiation in females than in males, indicating male‐biased dispersal in the Omei tree frog. Considering the life history reported in this species, we discussed potential mechanisms driving the male‐biased dispersal in the Omei tree frog.