In this study, leptin gene was chosen as a candidate gene to evaluate its effect on litter performance traits in four indigenous pig population of Anhui province in China. Two SNPs (U_66254 g.3469 T>C; g. 3714 G>T) in Exon 3 of leptin gene were demonstrated by PCR-SSCP and sequencing of PCR product. Litter performance traits including Numbers of Born Alive (NBA) of the first parity and latter parities were recorded in four pig breeds population. The further association analysis of the 2 SNPs with litter performance traits were conducted in four pig breeds population including 213 sows. Researchers found the 2 SNPs are significantly associated with litter performance traits. The effect of CC genotype of SNP (U_66254 g.3469 T>C) and TT genotype of SNP (U_66254 g.3714 G>T) were significantly higher than other genotypes in both litter traits (p<0.05). The study suggested that lepetin gene could be used for marker assisted selection program as a molecular genetic marker for litter sizes in Chinese indigenous pig breeding.