Genetic relationships were examined among a total of 74 lancelets, Branchiostoma japonicum (Willey 1897), collected at 16 stations in the Seto Inland Sea on the basis of the sequence of the COI region of mitochondrial DNA. Genetic divergence was usually high at the stations near straits. Besides, there were no significant relationships between geographical and genetic distances of individual lancelets. As many as 62 haplotypes were recognized, among which only three comprised multiple individuals from distant stations, and the remaining ones comprised a single individual. In a dendrogram, some clusters were made up of individuals from nearby stations whereas other ones were made up of those from more or less distant stations. These results suggest that the high genetic heterogeneity of the lancelet population in the Seto Inland Sea is maintained by continuous genetic exchanges via a large-scale dispersion at long planktonic stages driven by tidal and constant currents in this region.