Abstract We examined the impact of Pleistocene glacial cycles on geographical distribution and genetic structure of the mitten crab Eriocheir sensu stricto in East Asia using sequence variation of mitochondrial cytochrome c oxidase I and cytochrome b gene segments. Phylogenies revealed four distinct but shallow structured lineages in Eriocheir s. s. Three lineages dominated the East China Sea-Yellow Sea, the Sea of Japan and the South China Sea on the margins of the region, and one lineage occurred on Okinawa Island. This geographical distribution represents a general phylogeographic pattern in East Asia, which is closely associated with the fluctuations of marginal seas and islands during the Pleistocene. The four lineages are estimated to have diverged during the mid-Pleistocene. Demographic expansions were observed in each lineage, starting within the second-to-latest interglacial period in the marginal sea lineages (∼70–130 ka) and within the last glacial period in the Okinawa lineage (∼25–80 ka). Expansions have probably taken place northward along the coast of the East China Sea-Yellow Sea, following the rise of sea levels. Centered on the southern Korean Peninsula, expansions have likely occurred northward along the west coast and eastward along the south coast of the Sea of Japan. Each marginal sea has served as a single refugium during glacial periods. Two secondary contact regions were identified, one of the East China Sea-Yellow Sea and South China Sea lineages, and another of the East China Sea-Yellow Sea and Sea of Japan lineages. Phylogeography of Eriocheir s. s. provides insights into the evolutionary history and mechanism for generating biodiversity in East Asia.