The phylogenetic relationships among subspecies of Pomatorhinus ruficollis are not clear. In this paper we sequenced two mitochondrial genes (Cyt b and ND2, in total 2 184 bp) and examined twenty individuals representing ten of the eleven subspecies of P. ruficollis in China. Molecular phylogenetic trees were reconstructed using maximum parsimony, maximum likelihood and Bayesian inference methods, with P. ruficollis and P. schisticeps as in-groups, P. montanus, P. ochraceiceps, P. ferruginosus and Xiphirhynchus superciliaris as out-groups. Results indicated that P. ruficollis was paraphyletic, in which P. schisticeps was embedded, and was divided into three phylogeographic groups: southwestern China group, southeastern China group and central China group. Our results also suggested discordances between phylogenetic relationships and morphological characteristics, and clarified some intraspecific taxonomic debates.