Abstract: The aim of the present study was to investigate the association of the polymorphism of HSL gene with carcass traits in native pig breeds in Guizhou province. Two native pig breeds in Guizhou province, Nuogu pig (n=30) and Luobo pig (n=50), were chosen with the crossbreed of Large White×Landrace (n=30) as control. The polymorphism of HSL exon 1 was detected by restriction fragment length polymorphism (RFLP) method. Three genotypes, AA, AB and BB, were detected from the HSL gene in three pig populations. It showed that A allele was dominant in the two native pig breeds with 60% in Nuogu pig, 89.5% in Luobo pig and the B allele was detected mainly from the European crossbreed with 91.7%. Compared with B allele, a single nucleotide mutation (G/A) was confirmed in A allele at the 442 bp of the coding region in exon 1 of HSL gene which resulted in the amino acid change from valine to isoleucine. Moreover, the lean percentage, backfat thickness and loin eye area of individuals with BB genotype were significant superior than that with AA genotype (P<0.01). These results indicated that the B allele committed to improve the lean percentage and loin eye area, and decreased the backfat thickness. It suggested that HSL gene could be a molecular marker for the selection of lean percentage in the native pig breeds.