In order to analyze the single nucleotide polymorphisms (SNPs) in the extron 2 of heart fatty acid binding protein gene (H-FABP) and its relationship with some meat quality traits in Merino Sheep (Ovis aries var. Merino), and to provide a theoretical foundation for the marker-assisted selection, we measured intramuscular fat (IMF) content, muscle fiber diameter and muscle fiber density of 150 Merino sheep, and used polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) technique to analyze the SNPs at the exon 2 of the H-FABP gene. It was shown that the exon 2 of H-FABP gene displayed AA, AB and BB genotypes. There were mutation of 939(A/G) and deletion of C in both AA and BB genotypes, and 789 (T/C) in BB genotype, which led to valine convertion to alanine. The BB genotype was advantageous genotype of IMF and there were significant difference between BB and AB (P<0.05), and extremely significant difference (P<0.01) between BB and AA. The correlation of BB genotype and muscle fiber diameter was negative. These results indicate that the exon 2 of H-FABP gene of Merino Sheep shows polymorphism and that H-FABP gene may be a major gene or a major gene-linked gene for meat quality of Merino Sheep.