We evaluated the correlation of scale genes (ant, eda, edar, fgfr) with four growth traits in common carp(Cyprinus carpio). A total of 155 microsatellite markers were selected from the homologous sequence of the carp genome. We used 116 progeny from a self-bred line of F1 derived from intercross lines of German mirror carp (Cyprinus carpio L.) and Amur wild carp (Cyprinus carpio haematopterus). We estimated the following genetic diversity parameters: allele number(No), effective allele number(Ne), observed heterozygosity(Ho), expected heterozygosity(He) using PopGene (Version 1.32). We used achi-square test to test for Hardy–Weinberg equilibrium. Of the 155 markers, 36 microsatellite loci were polymorphic with 2–4 alleles for each locus (86 alleles for the 36 loci). The mean number of alleles and the mean effective number of alleles were 2.388 9 and 2.209 4, respectively. The mean observed heterozygosity and expected heterozygosity were 0.624 5 and 0.529 2, respectively. The mean polymorphism information content (PIC) was 0.432 1 for the 36 loci, of which 23 loci had a moderate level of polymorphism (0.25≤ PIC<0.5) and 13 loci had a high level of polymorphism (PIC≥0.5). Our results suggest the population has a moderate level of polymorphism. Given that the microsatellite markers were located in the genes or their contexts, the level of polymorphism may be even lower. The majority (69%) of the 36 loci deviated significantly from Hardy–Weinberg equilibrium. The artificial selection pressure and development of the self-bred line may explain this phenomenon. Of the 36 markers, 10(28%), 7(19%), 7(19%), and 11(31%) were significantly associated with body weight, body length, body height, and body thickness, respectively. Eleven dominant genotypes were identified via the multiple comparisons. The higher screening rate of SSR markers tightly linked with growth traits demonstrated that the scale genes maybe associated with growth traits.