We investigated the phylogeography of the Asian brackish water clam, Corbicula japonica, to clarify its demographic history using partial mitochondrial COII gene sequences (990 bp) from 283 individuals collected from around the Japanese archipelago and adjacent areas. Phylogenetic analyses revealed the presence of two major groups within our samples: monophyletic Group I comprising Lineages A-E of C. japonica and paraphyletic Group II consisting of Corbicula sp. Lineages A-C were distributed in Japan and Sakhalin Island, and Lineages D, E, and Corbicula sp. were distributed in the Korean Peninsula. Nested clade analysis (NCA) revealed that Lineage A—the dominant lineage in Japan—consisted of Pacific and Japan Sea lineages, the latter comprising southern and northern Japan Sea groups. Genetic diversity indices of the southern group were higher than those of the northern group, suggesting historical range expansion in the Sea of Japan from southwest to northeast. Geographical distribution of these genetic groups appears to have been influenced by major ocean currents around the Japanese archipelago. Dominant haplotypes in the star-shaped haplotype network of Lineage A were distributed throughout the entire distribution range of each genetic group, implying rapid range expansion of this species. The results of mismatch distribution analysis and molecular clock estimation suggest that expansion of lineage A occurred during the late Middle or Late Pleistocene. In contrast, restricted or past gene flow suggested by NCA and the many unique haplotypes (110/123; 89.4%) present in Lineage A suggest that gene flow among extant populations is rather limited.