Revealing cryptic biodiversity and understanding their evolutionary histories is important to predict how climate change promoted diversification. The marine gastropod Reticunassa festiva is a common species distributed along the coast of China Seas and possesses cryptic diversity. In the present study, the phylogeographic pattern of R. festiva is investigated to test the potential mechanism that drove its diversification in China coastal regions using the mitochondrial cytochrome oxidase subunit I (COI) and nuclear 28S rDNA sequences. Three highly divergent COI clades (Clades A, B, and C) with considerable differences in genetic distances, haplotype diversity, and nucleotide diversity among each other were identified. The estimated divergence time between the two dominant clades (Clades A and B) was 2.0711 Ma, corresponding to the third major cool period in the Pleistocene. The sea surface temperature fluctuation in the subtropical ancient East China Sea could be the major drivers for the diversification of the two R. festiva clades. It is also suggested that the distribution pattern of Clades A and B is shaped by two major ocean currents. This study provides evidence for the correlation between species diversification and climate change in the NW Pacific during the Pleistocene.