The distribution of Coreoperca kawamebari was known to be restricted to the Tamjin River and several small streams flowing into the southern part of the West Sea, while C. herzi was widely distributed throughout South Korea except the areas inhabited by C. kawamebari: the two species were known to be allopatric. However, we found that both species were sympatric in the Boseong River, a tributary of the Seomjin River, and the Jiseok Stream, a tributary of the Yeongsan River. Local-scale distribution of the two Coreoperca species, fish assemblages, and environmental variables were surveyed to investigate effects of environmental factors on fish community structures in the Boseong River. Rank abundance distribution of fish community at the study sites indicated that fish species diversity and distribution pattern of the two Coreoperca species were closely related to habitat diversity. The result of canonical correspondence analysis showed that C. kawamebari was distributed in pool areas while C. herzi was found in the areas with higher water velocity and boulder substrate. These results suggested that species diversity of fish community decreased and only one of the two Coreoperca species inhabited at the sites with less diverse habitat, but on the other hand, high habitat diversity increased species diversity and allowed the two species to coexist.