We used previously established molecular methods to determine how far the Asian invader nereidid worm Hediste diadroma has spread into northeast Pacific estuaries that are inhabited by the native congener H. limnicola. Further, we analyzed the mitochondrial DNA of 702 Hediste specimens collected from 27 estuaries along 1,350 km of coastline in Washington, Oregon, and California, USA, to distinguish between the morphologically indistinguishable immature stages of these two species. In total, 377 specimens were identified as the invader H. diadroma and 325 were identified as the native H. limnicola. The invader H. diadroma was dominant at many sites in Puget Sound, Washington, and in the Columbia River estuary, Washington, and Oregon, suggesting that this species initially invaded estuaries in Washington or northern Oregon. In contrast, the native H. limnicola was dominant at intertidal sites in California and at subtidal sites in the Columbia River estuary. We also analyzed a partial nucleotide sequence from the mitochondrial cytochrome oxidase subunit I gene of H. diadroma in specimens collected from seven sites in the US and 11 sites in Japan, which showed no marked geographic differentiation between 18 US and 31 Japanese haplotypes. This finding suggests that H. diadroma have been introduced repeatedly into US estuaries from many regions in Japan.