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Macrophytes play a major role in the structuring of aquatic environments and may influence the distribution and feeding habits of fish species. We explored the microhabitat characteristics influencing the spatial distribution of newly discovered <i>Coreoperca kawamebari</i> (Temminck & Schlegel, 1843) in the upstream reaches of the Geum River. Out of 21 study sites, <i>C. kawamebari</i> was found in 10 sites, and its abundance was strongly positively correlated with “vegetated” microhabitats, especially those covered by elodeids (e.g., <i>Ceratophyllum demersum</i>). The utilization of elodeids by the piscivores fish, <i>C. kawamebari</i>, may limit the abundance of other native fishes, and stable isotope analysis also showed that <i>C. kawamebari</i> is likely to consume other fish species. However, the influence of other fish species on <i>C. kawamebari</i> is assumed to be small, considering that <i>C. kawamebari</i> is a latent predator. Although the abundance of other fish was low within the preferred microhabitat of <i>C. kawamebari</i>, other species were abundant in each site where <i>C. kawamebari</i> was dominant. From this finding, we conclude that the successful settlement of <i>C. kawamebari</i> in the upper section of the Geum River can be attributed to their habitat preferences. Although the elodeids favored by <i>C. kawamebari</i> generally have difficulty developing in the upstream section, the habitat creation by humans has contributed to the stable settlement of new fish species.