We investigated the molecular phylogeny and genetic differences among local populations of Korean Hemiculter fishes based on their mitochondrial cytochrome b gene sequences. Our results indicated that Hemiculter leucisculus populations in China were clearly divided into two groups. The first group (Group 1) included the populations of the Yangtze River and its surrounding areas (including the Qiantangjiang, Lingjiang, Jiulongjiang, and Minjiang rivers); the second group (Group 2) contained local populations from southern China (including the Nanliujiang, Zhujiang, Wanquanhe, Qianjiang, and Nandujiang rivers). The Korean Hemiculter eigenmanni differed in its cytochrome b gene sequence by 0.6-1.0% from the Chinese H. leucisculus (Group 1), which inhabited the Yangtze River and its surrounding areas, suggesting they were phylogenetically close and likely to be the same species. The Korean H. leucisculus differed from the Chinese H. leucisculus (both Groups 1 and 2) by 8.1-9.5%, indicating a very distant phylogenetic relationship; however, the Korean H. leucisculus differed from Hemiculter bleekeri by only 0.5-0.7%, showing intraspecific nucleotide differences. We conclude that the taxonomic relationship between the Korean H. leucisculus and H. bleekeri requires further investigation using type specimens.