We investigated the geographic population structures of two intertidal kinorhynch species, Echinoderes sensibilis and Echinoderes sp. A, in the vicinity of Tsugaru Strait between Honshu and Hokkaido Islands, Japan, to examine whether the distribution or connectivity of populations of either species has been constrained by the strait. For each species, we examined the geographic distribution of COI haplotypes, constructed a median-joining haplotype network, and calculated statistics of genetic variation and connectivity. Tsugaru Strait is the northern range limit for E. sensibilis, which comprises a large, evolutionarily stable metapopulation that appears to have undergone a reduction in size followed by expansion; connectivity is low among most local populations, including across Tsugaru Strait. A divergent haplotype lineage showing no variation occurred only at Horozuki, suggesting recent immigration there from outside the study area. Echinoderes sp. A underwent a severe population bottleneck followed by rapid expansion. It occurred at all sampling sites on both sides of the strait, with high connectivity between populations across the strait. There is a zone of secondary contact between moderately divergent, presumably previously allopatric lineages in eastern Hokkaido. Present-day conditions in the strait have existed only for the past 8000 years, and differences in these species' distributions and apparent connectivity across the strait may relate to conditions existing in the strait when the species underwent population expansions or shifts in range; these historical events were not necessarily concurrent between the species, and occurred more than 8000 years ago. We discuss dispersal mechanisms for kinorhynchs, which could include suspension transport or rafting.