The maturation of marine phylogeography depends on integration of comparative information across different regions globally. The northwestern Pacific, characterized by unique tectonic setting, however, is still underrepresented. This study seeks to highlight its phylogeographical history based on the available population data, focusing on three seas: the East China Sea (ECS), the South China Sea (SCS) and the Sea of Japan (SOJ). We first conducted a literature survey to evaluate current research efforts and then reanalysed the population structure, historical demography and genealogy for two selections of studies (namely ‘the ECS category’ and ‘the multiple-sea category’) to elucidate the evolutionary processes within and across the seas, respectively. For the ECS category, the meta-analyses revealed most studies displayed a shallow phylogeny, indicating a single origin from the sea. Significant population structure was commonplace, particularly in molluck and crustacean studies, with proportions of 89% and 80%, respectively. Nearly all studies selected showed signals of population expansion: the times estimated were closely linked to a period of ~120–140 Kya rather than the last glacial maximum. For the latter category, divergent intraspecific lineages appeared among seas and overlapped in the adjacent regions, a pattern implying each sea had served as an independent refugium during glaciations. The genetic splits, however, were estimated to arise from separate events dating from late Miocene to middle Pleistocene. As phylogeography is still in its infancy in the region, more effort is needed to test and complement the general rules abstracted here. Finally, challenges and prospects were discussed to accelerate further research.