Milk protein gene polymorphism is an important component for studying genetic diversity in conservation of domestic animals. Milk processing properties depends on casein protein components which are controlled by casein cluster genes in animals. The domestic yak (Bos grunniens) is a long-haired domesticated bovid found throughout the Himalayan region of Southern Central Asia. Yak milk is used to prepare cheese, curd and other fermented products. Yak populations present in Indian states of Ladakh, Himachal Pradesh, Sikkim and Arunachal Pradesh were analysed for polymorphisms of β-casein and κ - casein gene regions based on DNA sequencing and SNP detection. Polymorphism occurring within exon VII of β-casein gives rise to A1 and A2 type alleles in cattle. κ- casein gene was found to be polymorphic in Indian domestic yak, which could be useful in genetic variation studies.