Patelloida pygmaea is one of the most abundantly distributed intertidal marine gastropods along the China coast. The mitochondrial (COI) and internal transcribed spacer 1 (ITS1) DNA of P. pygmaea, one hundred and thirty-seven samples collected from 13 localities along its distribution along the China coast, were used to investigate the phylogeographic patterns of P. pygmaea. Phylogeographic analysis revealed three distinct phylogeographic clades, the South China Sea (SCSC), the Bohai and Yellow Sea (BYSC), and the East China Sea (ECSC) clades. The results of AMOVA showed significant genetic differentiation (P < 0.001) among the three clades. The vicariance of the three lineages was created by the glacial drop in sea level, the Changjiang Estuary, and the sea surface temperature gradient. Based on the ITS1 gene, the BYSC clade was split into two subclades, the north and south clades. We speculate that the Shandong Peninsula was another possible barrier limiting gene flow in the BYSC. Ocean currents played more roles in influencing gene flow within the three clades. The mismatch analysis confirmed the demographic population expansion (P > 0.05). Phylogeographic patterns of P. pygmaea have been primarily affected by Pleistocene climatic oscillations and environmental conditions. During the glacial periods, the sea regressed and moist and warm conditions, characterizing glacial refugia, became prevalent in the region and caused isolated P. pygmaea populations to expand.