This study assessed the genetic outcomes of reintroducing Zacco koreanus into the Bongseonsa Stream by comparing the genetic diversity and population structure of the reintroduced population to those of the original populations from the Jojong and Sudong Streams. The reintroduced population in Bongseonsa Stream retained multiple haplotypes and displayed a mixed genetic composition with the original populations, indicating the reintroduction strategy’s effectiveness. The pairwise genetic differentiation value (FST) suggested that the Jojong Stream population, which is geographically closer and ecologically similar, contributed more to gene flow and potential local adaptation in the reintroduced population. Results from STRUCTURE analysis (K=2) and principal coordinate analysis (PCoA) showed no clear genetic separation among populations, supporting effective genetic integration. However, the relatively small effective population size (Ne) of the reintroduced population raises conserns about potential longterm risks of inbreeding and genetic drift, which could lead to a loss of genetic variation. Overall, the reintroduction successfully established a genetically diverse population in the short term, but continuous monitoring and adaptive management are crucial for maintaining genetic health and ensuring long-term population stability. This study underscores the importance of integrating genetic considerations into freshwater fish restoration programs and provides a reference for developing sustainable population management strategies.