Barbus capito is an endemic species in the Aral Sea of Uzbekistan. It is well-known for its salt tolerance and fast growth, and is a valuable food source in the region. The species was introduced to China in 2003 and F1 was obtained using artificial propagation in 2010. As an introduced species, B. capito has the relatively limited genetic resource due to the small founder population size. It is very important to effectively protect and utilize the existing gene resources in breeding practice. In this study, 24 microsatellite markers were selected to analyze the genetic structure in cultured F1 population including 96 individuals. A total of 74 alleles were detected and the length of fragments ranged from 109 to 367 bp. The number of alleles per locus was from 2 to 5, the mean was 3.0833. The effective number of alleles (Ne) ranged from 1.1445 to 4.6264 with an average of 2.2656. The observed heterozygosity (Ho) and the expected heterzygosity (He) varied from 0.1354 to 1.0000 (mean=0.5384) and from 0.1269 to 0.7881 (mean=0.4872), respectively. The value of polymorphic information content (PIC) was between 0.1183 and 0.7490 with an average of 0.4281, and this result indicated that the level of genetic diversity was moderate (0.25≤PIC＜0.50). The population accorded with Hardy-Weinberg equilibrium checking by ?? test except 8 markers including B1, B20, B32, B37, B45, B51, B68, and BC43. In addition, the correlation was analyzed between 24 microsatellite markers and growth traits using the GLM procedure of SPSS 19.0. As a result, there were 8 markers that had a significant (P＜0.05) impact on growth traits. Six markers including B1, B20, B45, B51, B59, and BC38 had a significant (P＜0.05) impact on body weight, length, height, and thickness. B26 had a significant (P＜0.05) impact on body weight, height, and thickness. BC3 had a significant (P＜0.05) impact on body weight and length. Superior genotypes were obtained using Duncan’s multiple comparison.