Endemic species are defined as taxa that naturally inhabit and grow within a specific area. Because they easily face regional extinction, continuous management is required. In this study, stable isotope analysis, length-weight relationships (LWRs), and condition factor (K) estimation were applied to oily bitterling Acheilognathus koreensis inhabiting three representative rivers including the Geum River basin, Seomjin River basin, and Tamjin River basin to compare ecological property and related biological conditions. Based on the corrected isotope value to account for difference in carbon isotope ratio (δ13C) of POM, Δδ13CA.koreensis-POM, estimated isotope niche areas of A. koreensis between Geum and Tamjin River populations were highly overlapped while those of the Seomjin River population were discriminated from other habitats, indicating differences in major diet sources among habitats. In addition, LWRs for the Seomjin River population showed a good growth with a b value of 3.155 compared to Geum and Tamjin River populations which showed relatively low growth rates of 2.888 and 2.968, respectively. Fluctuation of the K value of the A. koreensis tended to decrease with growth in the Geum River while that of the Seomjin River population exhibited the highest increasing trend. This study confirmed differences in diet resources among habitats for A. koreensis, which resulted growth and fatness variations for each population. Our results can be used as basic information for effective conservation and management strategies of A. koreensis populations.