This experiment was conducted to study the association of the polymorphism of partial Adipocyte Fatty AcidBinding Protein (AFABP) gene with the content of intramuscular fat and serum Triglyceride in ducks. A pair of primers Pin1 was designed according to the sequences of AFABP gene mRNA in duck and AFABP gene in chicken to amplify duck intron1 of AFABP gene, then 4 pairs of primers were designed according to the cloned gene. The SNPs were detected by PCRSSCP, confirmed by sequencing, then the association of polymorphism of AFABP gene with the content of intramuscular fat and serum Triglyceride was studied. The results indicated that the product by Pin1 included partial exon1, exon2 and complete intron1 of AFABP gene after clone and sequence, and homologous comparison was done between duck and chicken AFABP gene, which showed the homology was 75.1%. Three and six nucleotide mutations were found in the products by primer P1 and P3, respectively, which resulted in three and eight genotypes, respectively. The results of ChiSquare test showed that Cherry Valley duck and Sumu duck deviated from the HardyWeinberg equilibrium (P<0.01) except Jingding duck in P1 locus, and all of the three groups fit with it in P3 locus (P>0.05) , while the distribution of them was different in various groups (P<0.05 or P<0.01) at the same time. The least square analysis showed that the content of IMF and TG were significant difference in different groups (P<0.05), but the content of IMF had no significant difference between genotypes in P1 and P3 (P>0.05), only content of TG had significant difference in various genotypes in P3 and the ducks with CD genotype had higher content of TG than those with other genotypes (P<0.05). These results suggested that polymorphism in intron1 of AFABP gene have certain effect on TG content, also indicated that it needs further study to get a conclusion if these SNPs can influence the intramuscular fat trait in duck.