Daphnia pulex complex is composed of nine species. One of these species, panarctic D. pulex, has the widest distribution in the northern hemisphere. It has recently invaded into Africa and New Zealand. However, this species lacks strong genetic regionalism in spite of the worldwide distribution. It is also distributed in Japan and named “Mijinko” as one of representative zooplankton species. In the 59th ESJ meeting, we reported that Japanese populations of panarctic D. pulex reproduced by obligate parthenogenesis and consisted of only a few lineages. To examine their evolutional or historical origin, we collected samples from various regions in Japan (total 33 ponds) and reconstructed Bayesian phylogeny based on the mtDNA sequences (1838bp) including 12SrRNA, putative control region, tRNA-Ile, tRNA-Gln, tRNA-Met and ND5. We also determined genotypes of these specimens using 13 microsatellite loci. We found total four lineages. Among these, two lineages consisted of several haplotypes recorded only in Japan. Comparison of the mtDNA sequences suggests that these two lineages have genetically diverged in Japan after emigrated from North America at least thousands years ago. The other two lineages are likely invaded to Japan much more recently.