Abstract: The Taihu strain of Erythroculter ilishaeformis is a premium aquaculture species and is now widely cultivated in the Yangtze River Delta freshwater region. Under captivity, sexual dimorphism in somatic growth is very common with female being faster grower and having larger body size compared with male. Therefore, manipulating sex for all-female population of E. ilishaeformis can substantially increase aquaculture production and economic benefits. However, the key regulatory genes and mechanisms affecting sex determination and differentiation of E. ilishaeformis are still unclear and no gender-related molecular marker has been reported yet. Consequently, developing the technique for the monosexual production of E. ilishaeformis remains difficult in the breeding program at present. To develop the technology, the genetic diversity and genomic sexual dimorphism of the Taihu strain were analyzed by AFLP (amplified fragment length polymorphism) molecular marker technique. The sampling size was 20 male and 20 female individuals, respectively. A total of 319 loci were detected using 8 pairs of polymorphic primers. Of the 319 detected loci, 185 loci displayed polymorphism. By analyzing the distribution of the polymorphic loci in all the examined individuals, we discovered a locus that was only existing among male individuals and was absent among females. In consistent with this observation, no male individual was detected in the artificial gynogenetic group of the E. ilishaeformis, and the locus was not detected in the genome of all examined gynogenetic individuals. The results suggested that sex determination and differentiation in this species may be strictly controlled by genes located in that specific region, and that gender difference locus we detected can be used as a male-specific marker. Our statistical analysis showed that the percentage of polymorphic loci of Taihu strain was 57.99%, the observed number of alleles of Taihu strain was 1.5799±0.4943, the effective number of alleles of Taihu strain was 1.3859±0.3971, and the Shannon’s information index of the population was 0.3221±0.2987. These data indicated that the genetic diversity of Taihu strain is moderate and is maintained at a similar level (P=51.21%, Na=1.512±0.500,Ne=1.252±0.371,I=0.218±0.275) compared with the results obtained 10 years ago.