The objective of the present study was to investigate the polymorphism in Kappa-casein (k-CN), Betalactoglobulin (β-LG) (AB genotype) and 222, 193, 82 and 29 bp bands (BD genotype). AB genotype was the most frequent in all the screened buffaloes, followed by the AA, EE, BB and BD genotypes. The frequency of DRB3/HaeIII A, B, D and E alleles were 0.422, 0.411, 0.055 and 0.111, respectively. Association study revealed that there was significant difference for total milk yield (TMY) and milk yield in 300 days (MY300) among all the DRB3 genotypes. This study provides a basis for further investigation in other breeds of Indian buffalo.