hybrid common carp gynogenetic line including 68 individuals was used as mapping pane1. Markers wNinety-one SSR markers and 33 EST makers and 364 SNP markers were selected to analyze the genomic DNA of 68 progenies derived from common carp full-sib family. Twenty-seven loci were discovered that had significant impact on feed conversion efficiency and thirty-five loci were significantly related with body thickness (<0.05)while twenty seven loci had significant impact on body weight (<0.05). SNP0041 and SNP0044 were related with feed conversion ratio significantly (<0.01), contributing to 15% and 16%, respectively. These markers can be used as molecular marker assisting breeding. Markers were used to screen the protein and nucleotide database in the National Center for Biotechnology Information (NCBI) in order to find the homologies. Blasting results showed that HLJ253 is highly correlated (61%) with the gene encoding structural protein (ORF2) of zebrafish. SNP makers associated with three traits were sequenced on NCBI in order to find related genes and possible functions.