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The population genetic structure of the messmate pipefish,  Corythoichthys haematopterus , in the northwest Pacific was investigated based on the partial mitochondrial DNA cytochrome  b  (589 bp) and 16S rRNA (528 bp) region sequences of 108 individuals collected from six sites along the coast of the Japanese archipelago and one site on Mactan Island, the Philippines. A total of 60 and 28 haplotypes were obtained from the cytochrome  b  and 16S rRNA regions, respectively. Two genetically distinct lineages were detected: lineage A and B, which are separated by mean pairwise genetic distances of 23.3 and 14.1% in the partial cytochrome  b  and 16S rRNA genes, respectively. Such a huge genetic divergence between lineages, which is comparable to or even higher than the interspecific level, and the difference in their geographical distributions and habitat preferences suggests that they are distinct species, although there is no marked difference in their morphology. Haplotype network and gene and nucleotide diversity statistics indicate that the two lineages have different biogeographic histories: lineage A experienced rapid population expansion after a population bottleneck whereas lineage B has a long evolutionary history in a large stable population. In contrast, the levels of genetic variation among populations are relatively low in both lineages, probably because of frequent gene flow among populations resulting from the dispersal of pelagic larvae by the Kuroshio Current. These results indicate that past climatic events and contemporary oceanographic features have played a major role in establishing the population genetic structure of  C. haematopterus .   Electronic supplementary material  The online version of this article (doi:10.1186/2193-1801-2-408) contains supplementary material, which is available to authorized users.

Population genetic structure of the messmate pipefish Corythoichthys haematopterus in the northwest pacific: evidence for a cryptic species