Insulin-like Growth Factor 1 (IGF-1) is one of important genes controlling growth and development in animals. By comparing with exon1- partial intron 2- exon 3- partial intron 4 sequences of from six individuals of Genetically Improved Farmed Tilapia(GIFT) strain, we identified three SNPs on in this study, including intron1_A1307G, intron1_G1319T and intron3_C6T. PCR-RFLP was performed in intron1_A1307G and intron3_C6T genotypes detection on 121 individuals from five families of GIFT strain. The results of correlation analysis showed that intron1_A1307G was significantly associated with female fish weight gain and the ratio of body thickness/length (<0.05). The weight gain and thickness/length ratio of female fish with AA genotype were significantly higher than those of female fish with GG type (<0.05). However, the correlation of genotypes with those traits in male fish was not significant(>0.05). Intron3_C6T was significantly associated with weight gain in both male (<0.01). The weight gain of male fish with TT and CT genotype was significantly higher than that of male fish with CC type, while the weight gain of female with CT genotypes was significantly higher than that of female fish with TT. Intron3_C6T was also significantly associated with height/length ratio(<0.05) in female fish. The height/length ratio of female fish with TT and CT genotypes was significantly higher than that with CC(<0.05). In order to verify the performance of the screened markers in other families, we detected the correlation between intron1_ A1307G, intron3_C6T genotypes and weight gain among 417 individuals from 60 families of GIFT strain(averaging seven individuals per family), and similar results were observed. The diverse genetic background and smaller size of samples resulted in the decreased correlation significance. These results showed that genetic background and sample size should be considered during molecular maker screening. And the two molecular markers of intron1_ A1307G, intron3_C6T identified in this study could be used as reference in GIFT strain breeding.