Feed conversion ratio is very important economic traits. The improvement of it can not only save the feed, reduce the cost, but can also improve the ecomonic efficiency. There were a great deal of studies relating to feed conversion ratio of QTL in the field of farming. But few were reported on fish, especially on common carp. The linked markers and genes from the analysis of QTL are very important tools for fish breeding. Seventy ESTSSR markers were selected to analyze the genomic DNA of ninetytwo progenies derived from the common carp (Cyprinus carpio L.) fullsib family, which come from the cross between progenies of Barbless carp and Hebaocold tolerance red carp. 70 makers segregate according to Mendel's Law, of which 48 segregate in 1∶〖KG-*2〗1 model and other 22 in 3∶1 model. Ma kers of “1∶1” segregation model were used to made marker regression analysis based on pseudotestcross strategy using Windows Map Manager 2.0. Six loci were discovered that had impact on feed conversion efficiency (HLJE335，HLJE25，HLE547，HLJE92，HLJE203，HLJE231) and two of them had a significant impact on this trait. ESTSSR markers were used to screen the nucleotide and protein database in the National Center for Biotechnology Information (NCBI) in order to find the homologies. High sequence homologies of HLJE547 marker were observed with the nucleotide sequence of ATPase, H⁺ transporting, lysosomal gene of zebra fish and protein sequence of zebra fish ATPase, H⁺ transporting, lysosomal protein. Homologous were 74%, 94% respectively. ATPase, H⁺ transporting, lysosomal protein is a component of vacuolar ATPase (V-ATPase), which were detected in iontransporting epithelium of the a blowfly rectum. In addition, there were a great deal of lysosome in epithelium of the Tachypleus tridentatus Leach rectum. Fish as the first key link of craniota may have some similar function with invertebrate. This indicates that V-ATPase may affect the function of digestive system through affecting the H⁺ transporting on lysosomal, which needs to be proved for further study.