Abstract: AFLP molecular marker technique was utilized to analyze the genetic differences among Erythroculter ilishaeformis, Ancherythroculter nigrocauda and their hybrid F1 (E. ilishaeformis♀×A. nigrocauda; 12 individuals each). A total of 257 bands were obtained by 9 primer combinations, and the percentage of polymorphic loci was 51.36%. There were 24 specific bands in the three populations. There were 15 shared specific bands between the A. nigrocauda and hybrid F1, and 2 were between the E. ilishaeformis and hybrid F1. There were 7 specific bands of E. ilishaeformis. The Shannon's information indexes of A. nigrocauda, E. ilishaeformis and hybrid F1 were 0.2326, 0.0794 and 0.1774, respectively. The Nei's gene diversity indexes of the three populations were 0.1602, 0.0537 and 0.1229, respectively. The expected heterozygosity among the three populations was 0.1582, 0.0464 and 0.1062, respectively. The genetic distance was 0.0523 between the A. nigrocauda and hybrid F1 and was 0.2165 between the E. ilishaeformis and hybrid F1. The genetic similarity coefficients between the A. nigrocauda and hybrid F1 was 0.9490, and it was 0.8053 between the E. ilishaeformis and hybrid F1. These data showed that the hybrid F1 was more homogeneous to the male parent of A. nigrocauda.