Abstract: In order to understand the current status of C.auratus germplasm resources in the Pearl River, we used the mitochondrial cytochrome c oxidase subunit Ⅰ (COⅠ) gene to examine the genetic diversity and population structure from eight localities in the Xijiang River. High genetic diversity was detected in C.auratus population. Statistically significant genetic differentiation existed among different populations (F_ST=0.164, P<0.001). Geographic distance and living habit of C.auratus might act as the potential factors that lead to significant population differentiation. In addition, neither neutrality tests nor mismatch distribution analysis find signals of recent population expansion.