Abstract: Small heterodimer partner gene is expressed in liver, heart, pancreas and adipose tissue and influences the lipid homeostasis. Three genotypes (GG, GA and AA) of SHP gene exon 1 were identified by PCRSSCP and their distribution was significant different (P<0.05) in five pig breeds (Large White, Landrace, Pietrain, Jinhua and Wild boar) by Chisquare analysis. The homozygotes were sequenced and one polymorphic locus (G374A，DQ002896) was found which changed the amino acid from Arg to His. Moreover, association analysis of SHP polymorphism with backfat thickness and intramuscular fat contents was conducted in the F2 generation from the Jinhua×Pietrain resource family. The results showed that the pigs with genotype AA had 27.0%, 30.6%, 19.5% and 40.9% lower backfat thickness at three positions (should, thorax-waist and buttock ) and intramuscular fat contents respectively than those with genotype GG (P < 0.05); At 6th-7th rib backfat thickness, the pigs with genotype AA was significantly lower than those with genotype GA by 23.0% (P <0.05).