We studied the phylogeography and genetic diversity of the pine sawyer Monochamus alternatus (Hope) (Coleoptera: Cerambycidae) to understand its colonization dynamics, potential for further invasion, and potential species divergence. This species is the main vector of the pine wood nematode Bursaphelenchus xylophilus (Steiner and Buhrer), which is the causative agent of pine wilt disease in Japan. The genetic structure was studied using sequences of mitochondrial DNA and microsatellites. The phylogenetic analysis revealed two distinct lineages within M. alternatus. There is no clear boundary between haplotypic distributions of the two clades. Coalescence should have been extended by population subdivision. There might also be a fusion of the two distinct populations, and both are completely saturated. Analysis of the microsatellite genotypes of populations in Japan showed a complex genetic structure. Estimates of overall population differentiation (F_ST) were significantly different from zero. The populations are thought to be at demographical nonequilibrium or to show restricted gene flow among prefectures. Although neighboring populations often had similar genetic compositions, significant isolation by distance in the total population was not detected. It is suggested that population expansion may have occurred not only by natural dispersal on a small scale, but also by long-distance dispersal likely enhanced by the relocation, (by humans) of infested wood. Our data suggest that M. alternatus is a species capable of dispersing over a large area, and therefore, multiple invasions of M. alternatus from distant areas is a possibility.