Abstract: The Calpain3 (CAPN3) gene, located within the confidence interval of the Quantitative Trait Loci (QTL) affecting meat tenderness, being regarded as a candidate gene for meat tenderness in cattle. In this study, SNPs in exon 23-intron 23 region of the yak CAPN3 was investigated from 1032 yak with Polymerase Chain Reaction-Single Strand Conformational Polymorphism (PCR-SSCP). Three Single-Nucleotide Polymorphisms (SNPs), resulting in three novel alleles were detected in this region, respectively. These variations included one synonymous in exon 23 and two SNPs in intron 23. Allele C was the most common allele (63.18%) in all of yak. These SNPs are the first report in yak CAPN3 and also suggest further analysis is required to explore the relations between variation sites and meat tenderness.