The genetic population structure of the mudskipper Boleophthalmus pectinirostris was investigated based on nucleotide sequence data from the mitochondrial control region (472 bp) of 131 individuals collected from four localities in Ariake Bay, two in Yatsushiro Bay, Kyushu, Japan, one in Korea (Suncheon) and one in China (Zhe Jiang). A total of 53 composite haplotypes were observed from 49 permutation sites. The estimated haplotype tree and pairwise Fst showed genetic differentiation among the Suncheon, Zhe Jiang and Japanese populations. The structures of the haplotype tree and network, and low genetic diversity of the Japanese populations compared to that at Zhe Jiang suggested that a bottleneck effect had occurred in the former after being isolated from the continental population by rising sea levels (i. e., relictual species). Based on the number of unique haplotypes in the Japanese populations and nucleotide substitution rate, the estimate of the divergence time for the Japanese and Zhe Jiang populations was much greater than that expected for the apparently relictual species distributed in Ariake Bay. The Ariake and Yatsushiro populations formed a single group in the haplotype tree, although the estimate of pairwise Fst showed a significant difference between the populations, probably associated with the differences in frequency of the most dominant haplotype. Accordingly, the two populations seemed to be genetically differentiated from each other, probably due to the geographical isolation.
