In this study, we conducted association analysis between microsatellite markers and growth traits such as body weight, total length, body length, body height, body thickness, head length, snout length, caudal stalk height and caudal length in the F₃ population of pikeperch (Sander lucioperca), the fast-growing strain, to identify markers for genetic breeding. The average allele number for each marker was 4.5. The average observed heterozygosity at 0.746 (ranging from 0.520 to 0.954), with expected heterozygosity recorded at 0.691 (with a range of 0.441 to 0.851). The average polymorphism information content was 0.641. The results showed that 38 microsatellite markers had significant association with at least one trait (P<0.05), among which 21 markers, such as HLJSL018, HLJSL021 and HLJSL022, had extremely significant association with the corresponding trait (P<0.01). Specifically, we detected several 2-21 significant microsatellite markers for 9 traits, ranging from 2 to 21, of which only two markers (HLJSL039 and HLJSL042) were identified for body length (P<0.05)； but there are 21 markers significantly associated with the height of the tail stalk, among which 11 markers such as HLJSL018, HLJSL021, and HLJSL022 are highly significant (P<0.01). There are 8 markers significantly associated with body mass, of which HLJSL018 and HLJSL067 are highly significant (P<0.01). A total of 195 dominant genotypes, with a proportion of over 5% higher than the overall mean, were obtained in 38 markers. Each marker obtained 1-10 dominant genotypes, among which HLJSL073 obtained the least dominant genotypes and HLJSL079 obtained the most dominant genotypes. In summary, we assessed the genetic structure of the pikeperch breeding population and identified markers closely associated with growth traits, which can inform the genetic selection of pikeperch.