Abstract: In this study, 149 polymorphic markers were screened from 200 microsatellite markers. From a family of mirror carp, which included 107 individuals. All samples were analyzed for body correlation, and intermuscular bone number was tested using the General Linear Model (GLM) single marker regression. Determination of the threshold values by 10,000 permutation tests showed that eight markers had significant correlation (P<0.05), in which HLJ3086, HLJ3642 and HLJ3515 had very significant correlation with intermuscular bone number (P<0.01). In addition, the genotypes of the captured correlative loci were determined by Duncan’s test using SPSS17.0 software. Markers were used to screen the protein and nucleotide database in the National Center for Biotechnology Information (NCBI). Blasting results showed that HLJ2891 was highly correlated (92%) with latrophilin-2-like and HLJ3515 was highly correlated (81%) with serine/threonine-protein kinase 32B-like of zebrafish. These functional markers and genotypes may provide an efficient basis for marker-assisted selection of intermuscular bone number in mirror carp.