The Japanese gnomefishes Scombrops boops and S. gilberti closely resemble each other but their geographical distributions in the northwestern Pacific Ocean are markedly differ- ent. In order to understand the determinants of reproductive isolation, we examined habitat use in relation to the reproductive strategy employed by these species in the Izu-Islands region, where adults of both species coexist. We examined the species compositions of the gnomefishes based on mitochondrial sequence differences, and the maturation process of gonads using the gonado - somatic index (GSI) and by histological observation of the gonads. Genetic analysis showed that large individuals (>400 mm SL) of both species were present in the region, whereas all small gnomefish (<400 mm SL) were identified only as S. boops. Thus, the Izu-Islands region is likely utilized as a nursery by S. boops but not by S. gilberti. The GSI of adult S. gilberti showed signif- icantly higher values in March compared to the consistently low values detected for S. boops. In addition, the GSI-elevated S. gilberti had mature ovaries and testes. These results suggest that the Izu-Islands region is utilized as a spawning ground by S. gilberti but not by S. boops. It appears that S. boops spawns in the upper reaches of the Kuroshio Current and that the offspring are trans- ported to the Izu-Islands region by the current. The differences between the species-specific spawning grounds, in conjunction with the transport provided by the currents, likely determine the interspecific differences in geographical distribution.