The enzyme citrate synthase (E.C.2.3.3.1) exists in nearly all living cells and stands as a pace-making enzyme in the first step of the tricarboxylic acid cycle (TAC).Citrate synthase is located within eukaryotic cells in the mitochondrial matrix.In this study,genomic fragments of the citrate synthase gene were amplified based on the sequences of one available contig in the EST-SNP database of grass carp.Two SNPs mutations,A-386G and C-499G,were identified after sequencing the PCR products.The two SNPs were located in intron ten of the citrate synthase gene.Regarding the two SNPs,the genotype and gene frequency of 144 grass carps were further assayed with the method of Snapshot.The frequencies of AA,AG and GG were 47.10%,38.41% and 14.49% at the A-386G site,and CC,CG and GG were 31.85%,46.67% and 21.48% at the C-499G site,respectively.The polymorphic information content (PIC) of the two SNPs were medium genetic diversity.A general linear model was used for the correlation analysis between the citrate synthase gene SNPs and growth traits (body weight,body length,body depth,head length,caudal peduncle length and caudal peduncle depth).The different genotypes of the A-386G and C-499G site were different but not significantly different associated with the six growth traits (P＞0.05).Seven diplotypes consisted of the two SNPs (remove minor allelic frequencies lower than 3% of the D2 and D5) were used to do the correlation analysis between the six growth traits.Association analysis indicated that five diplotypes were not significant different growth traits (P＞0.05),except for head length (P＜0.05).The diplotypes D6 (A-386G/AG and C-499G/GG) had the maximum mean of all growth traits,suggesting that D6 belongs to dominant genotypes.These results indicate that the two SNPs of citrate synthase gene can be used as a molecular marker for growth traits selective breeding in grass carp.