Abstract: The purpose of this study was to separate three genetic variants ofβ-lactoglobulin ( β-Lg) in bovine milk using capillary electrophoresis ( CE) , in order to provide method for milk quality control. Whey samples were prepared from whole milk of yak, cattle- yak and Tibetan Yellow cattle, and analyzed by polyacrylamide gel electrophoresis ( PAGE) and CE, respectively.The results showed that both CE and PAGE could separate the three genetic variants of β- Lg; the analysis of yak milk samples added with different proportions of cattle- yak milk showed that CE method was able to detect as low as 5% of added cattle- yak milk with excellent linear relationship.In addition, the analysis of two genetic variants ofβ- Lg in Tibetan Yellow cattle with heterozygous genotype of β-Lg showed that CE method could more accurately determine the relative proportion of β-Lg A andβ-Lg B than PAGE.The results of this study indicated that CE method could effectively separate and quantify the three genetic variants of β-Lg and has potential applications in yak milk quality control.