1. Although Sinodiaptomus valkanovi [sensu Ueda & Ohtsuka (Hydrobiologia, 379, 1998, 159)] is one of the most common freshwater calanoid copepods in Japan, it was originally described from specimens collected in Sofia, Bulgaria, as a subspecies of S. sarsi. This original description raises two issues requiring further investigation. One is whether or not S. valkanovi should be differentiated from S. sarsi at a species level, and the other is whether or not records of S. valkanovi from outside of Japan are the result of biological invasions. 2. We examined the gene flow between S. valkanovi and S. sarsi in Japan, using nuclear DNA (the ribosomal internal transcribed spacers 1 and 2 plus the intervening 5.8S ribosomal DNA subunit) sequence to clarify if these two taxa are separable at a species level. We also investigated the population genetic structure of S. valkanovi in Japan, using the mitochondrial cytochrome c oxidase subunit I (mtCOI) gene, and subsequently of two recently discovered New Zealand populations, to elucidate the origin and colonisation/invasion history of this taxon. 3. In total, 43 and three Japanese populations of S. valkanovi and S. sarsi, respectively, were analysed. These two taxa did not occur together in any of the localities. Nuclear DNA analysis did not provide any evidence of gene flow between them, and the inter-taxon variability of mtCOI was high, corroborating the conclusion of Ueda & Ohtsuka based on morphological characteristics that S. valkanovi and S. sarsi should be differentiated at the species level. 4. In Japan S. valkanovi populations are segregated into two areas, around the Seto Inland Sea (SIS) and northeastern (NE) area. A distinct contrast in the genetic diversity was observed between the areas; five mtCOI haplotypes were recovered from the NE area while 38 were observed in the SIS area, despite a similar geographical range and number of individuals analysed in both areas. Furthermore, S. valkanovi in the SIS area possessed a mixture of both ancestral and derived haplotypes, while those in the NE area mostly consisted of derived haplotypes. These results suggest that the NE populations were founded recently by a limited numbers of individuals from SIS populations. 5. All specimens of S. valkanovi from New Zealand possessed one specific mtCOI haplotype. In Japan, this haplotype was found only in the NE area, suggesting the origin of New Zealand S. valkanovi. It is likely that this copepod has on several occasions invaded areas outside of Japan, one of which was associated with the original description of this taxon in Bulgaria.