Abstract: Gene pyramiding breeding is based on the effect of polygenic polymerization to change correlated character. In previous studies, growth-related markers were found in Siniperca chuatsi. Among them, five markers with six growth-favorable genotypes were selected, including two sites of single nucleotide polymorphism (SNP) located in GH gene and four sites of microsatellite (SSR):SC10, SC52, Sin135 and AP34-23. To get deeper insight into the effect of artificial breeding on growth-related markers identified in previous studies, we analyzed the number of favorable genotypes of these markers in five breeding generations of Siniperca chuatsi, Huakang No.1. By direct-sequencing and polyacrylamide gel electrophoresis, we found that the sum of two SNP favorable genotypes and four SSR favorable genotypes appeared pyramiding. The result showed that the number of total favorable genotypes ranges from 0 to 4 in the tested fishes. The average contents were 0.36, 0.71, 0.68, 0.77, 0.94 in F1, F2, F3, F4 and F5 generations, respectively, showing the number of favorable genotypes increased synchronously with the growth rate of the populations, which reflects that, artificial breeding has aggregated favorable genotypes in some degree. The SSR analysis showed that, when compared with F1, the genetic distances increased from F2 to F5 while the genetic similarity decreased, which observed objective law. When compared with its contiguous generation, the genetic distances decreased from F1 to F5 while the genetic similarity increased. The analysis of the genetic distances indicated that artificial breeding has conserved individuals of higher genetic similarity, which in performance have phenotypes of fast growth, heavier body weight or longer body length. The genetic diversity shows no large fluctuations, but a state of stability, which indicated further space for breeding.