Abstract: StearoylCoA desaturase (SCD) and Sirtuin 1 (Sirt1) on the chicken chromosome 6 are two functional genes that are associated with fat deposition In this study，single nucleotide polymorphisms (SNPs) were screened by comparative sequence analysis using DNA pool of three divergent chicken breeds including Taihe Silk, White Recessive Rock and Xinghua A total of 13 SNPs were identified in the SCD gene, of which 5 SNPs were in the coding region (2 missense mutations) and 10 SNPs were novel SNPs And 35 SNPs were identified in the Sirt1 gene including 10 SNPs in the coding region (2 missense mutations), 3 InDels and 18 novel SNPs The SCD c492 G>A and the Sirt1 c1753 G>A polymorphism were genotyped in six chicken breeds (White Recessive Rock, Xinghua, Taihe Silk, Baier Huang, Kangle, Nancheng Black) using single strandedconformation polymorphism (SSCP) assay The results showed that the genetic polymorphisms were abundant, providing new markers for further association analysis in this genomic region