Fatty Acid Binding Proteins are mainly involved in fatty acid transfer in the extracellular and intracellular membrane, and also take part in the regulation of cell growth and proliferation. In this experiment, two heart and muscle fatty acid binding protein genes，jlFABP3a and 3b, were isolated from Cyprinus carpio var. jian. Consistent with other FABP3s, jlFABP3s contain four exons and three introns. The open reading frames of 3a and 3b encode 133 amino acids share 93% and 94% similarity with each other in DNA and protein level, respectively. And there was clear difference in sequences and lengths between two genes introns. Twenty-six and twenty-five SNPs were found on jlFABP3a and 3b respectively in Cryprinus carpio var. jian population using alignment sequences from different individuals. And genotypes in 3 SNP loci were detected using PCR-RFLP. The SNP-weight gain correlation analysis indicated C30G was significantly associated with male juvenile, female juvenile and adult fish weight gain (P<0.05) in total experimental samples. Individuals with CC genotype grew faster than CG individuals. G267T was significantly related with female adult fish weight gain (P<0.05) in 5 families, and three genotype individuals had same growth trends in the 7 populations, though no significant (P>0.05). Taking two SNPs (G267T and C30G) into account, correlation analysis revealed individuals with GGCC grew the fastest in female and male fish, and grew 17% and 12% faster than GGCG ones. In the experimental samples，the GGCC individuals occupy only about 9%, indicating the presence of large selection space, and can be used as reference in molecular assistant breeding of Cryprinus carpio var. jian.