Dairy farms in India consists over 304 million cows and buffaloes; hence, considered the largest dairy herd in the world, with a production of 112.5 million tons of milk. Cattle of Kerala are mainly classified as crossbreed and indigenous. Milk is the soul source of any dairy products and thus important source protein, energy and micronutrients such as Ca, Mg, P and vit. B12. A1 and A2 are the two types of milk. BCM-7(Beta Casomorphin-7) which is believed to cause autism, schizophrenia and other non-communicable disorders is produced by digesting A1 milk. The main purpose of this study is to analyse the status of A1 and A2 alleles of a beta- casein gene in high-quality milk yielding cattle breed Vechur and high milk yielding exotic breed Holstein. Highquality DNA was extracted from the venous blood of the Vechur and Holstein cows and subjected to the PCR amplification of the Beta-Casein Gene. PCR products were visualized and sequenced. Sequence analysis was done for the genetic characterization of the gene in Vechur and Holstein cattle breeds. The sequences showed the characteristic difference in the nucleotides between the Vechur and the Holstein breed in the gene. In conclusion, the role of beta-casomorphin in physiological functions remains argumentative and we need more research to resolve the mechanism and study physiological functions of β-casomorphin and variation of the cow breeds in the world.