We used mitochondrial (cytb, 16S) and nuclear (ITS2, S71, RAG1) sequence data to assess the degree of genetic differentiation between the recently described lacustrine Hypomesus chishimaensis from the Kuril Islands and its anadromous congener H. nipponensis from Hokkaido, Japan. The results showed that the two species are not genetically distinct at these loci. Phylogenetic trees depicted an unstructured clade consisting of individuals of both species and sequence data showed haplotypes that are shared between putative species for all markers. We conclude that H. chishimaensis is an alternative life-history type of H. nipponensis that should not be recognized at either the species or the sub-species level.