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The spiny-flanked frog Quasipaa shini is distributed in southcentral China. Here, phylogenetic relationships and diversification of the species were examined using mitochondrial COI gene sequences of 70 individuals from eight populations. Phylogenetic analyses revealed that the species contained two deeply divergent clades (Clades I and II) and five subclades in Clade II. Haplotype network, AMOVA and genetic distance estimations also supported the separations of the six phylogroups. Based on the results, we proposed that at least the Clade I should represent a cryptic species. Neutrality tests indicated that all populations and clades have been probably suffered bottleneck effects or subdivisions.