Abstract: As a newly described candidate gene in obesity, FTO gene showed a strong and highly significant association with the obesity-related traits in various human populations. It has been suggested that FTO gene play a key role in the regulation of energy balance and feed intake. Here we sequenced the -2.0 kb of the 5' flanking region of the porcine FTO gene, 7 SNPs were detected in this region and genotyped on the Jinhua x Pietrain F2 reference population. Using a gene-wide haplotype-tagging approach, three tag SNPs were examined. The SNPs of g -1191 A>G had significant associations with Intramuscular Fat (IMF) content (p<0.05), but not with the Average Backfat Thickness (ABF), Leaf Fat weight (LF) or Average Daily Gain (ADG). Additionally, allele frequencies of the g -1191A>G mutation were studied in 6 pig breeds and the G allele was mainly occurred in Chinese native pig breeds. These results provided the solid evidence that FTO gene was associated with the intramuscular fat deposition in pigs.