The population structure of Bothrocara hollandi, a dominant deep-sea demersal fish in the Japan Sea, was analyzed on the basis of the nucleotide sequence of part of the mitochondrial control region. The 296 individuals analyzed were collected at 17 sites at depths between 375 and 1677 m, and could be divided into a distinct monophyletic group of haplotypes and a paraphyletic group that contained the remaining haplotypes. Individuals in the first group were collected only from shallower sites at depths less than 1100 m, and they were found predominantly off the western part of Honshu Island (the Japanese mainland). Individuals in the second group were collected from all sites at which fish were sampled. The genetic diversity of the first group was greater than that of the second group. As a consequence, the genetic diversity of populations showed a tendency to decrease with increasing depth. The divergence of the 2 groups was estimated to have occurred during the early part of the last glacial period. The geographical pattern of distribution of haplotypes might be attributable to the accumulation of unique genetic characteristics in different refuges during the last glacial period and to secondary contacts as a result of migration from such refuges after the last glacial period. No genetic differentiation between the 2 morphotypes of this species was detected. KEY WORDS: Phylogeography · Deep-sea demersal fish · Bothrocara hollandi · Japan Sea · Mitochondrial DNA Resale or republication not permitted without written consent of the publisher

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