Abstract: To better understand the polymorphism of ghrelin gene and its correlation with the growth performance of Nile tilapia (Oreochromis niloticus), we obtained the sequences of ghrelin gene by using PCR and sequencing, from DNA samples of two Nile tilapia populations. The two groups are the fast-growing population and the base population, and we used 40 DNA samples from each population. Dnasp v5 and MEGA 5.0 software were employed for the polymorphism analysis and the effective screening of SNP loci. We applied the snapshot method for SNP genotyping of the offspring of the two populations, and then analyzed the correlation between the growth index and the genotypes of SNP. We found that the base population had more SNP than the fast-growing population, but the average numbers of nucleotide differences (K) and nucleotide diversity (Pi) of the latter were higher than those of the former. There were three valid SNP loci in ghrelin gene and they were all located in the first intron. The genetic structure analysis demonstrated that the three SNP loci in the offspring of the two populations were low polymorphism loci (PIC0.25), but in hardy-weinberg equilibrium (P0.05). The genetic diversity parameters (observed heterozygosity, expected heterozygosity and polymorphism information content, etc) of the three SNP in the offspring of the fast-growing population were lower than those of the base population. The three SNP loci were the same in the genetic diversity parameters, the frequencies of alleles and genotypes, thus had complete genetic linkage. The offspring of the two populations had the same dominant genotypes of the three SNP loci. The offspring of the fast-growing population exhibited significantly higher frequencies of dominant genotypes than those of the base population. Moreover, we analyzed the correlation between the genotypes of SNP loci and the growth traits of the offspring of the two populations. There were significant differences between different genotypes (S1:GG AG, S2:TT AT, S3:AA AT; P0.05) in the growth traits including the body weight, the body length, the body height, the head length and the caudal peduncle depth. The growth traits (body weight, body length, body height, head and tail handle height) of D1 diplotype (S1: GG, S2: TT, S3:AA) were significantly higher than those of D2 diplotype (S1:AG, S2:AT, S3:AT). These results suggested that D1 diplotype of ghrelin gene was closely related to the growth performance of Nile tilapia, therefore it could be used as a potential molecular marker for better breeding.