A polymorphism of α-lactalbumin gene LAA exon Ⅰ, Ⅱ, Ⅲ, and IV has been identified by PCR-single strand conformation polymorphism protocol to reveal the distribution of diversity of α-lactalbumin in Maiwa yak at the molecular level. The sequences corresponding to the coding region of α-lactalbumin gene were used for phylogenetic analysis to establish the phylogenetic relationship of LAA variants in the Bos genus. Experimental results indicated that most yak milks were with hybrid genotype in exon Ⅰof α-lactalbumin. A new variant had been identified in Maiwa yak breed by resquencing analysis and entered into GenBank with accession number JN084189. The phylogenetic analysis presented α-lactalbumin evolution consistent with species at a degree.