Milk protein polymorphism plays an important role in genetic diversity analysis, phylogenetic studies, establishing geographical diversity, conservation decision, and improving breeding goals. Milk protein polymorphism in Indian goat breeds has not been well studied; therefore, an investigation was carried out to analyze the genetic structure of the casein gene and milk protein diversity at six milk protein loci in nine Indian goat breeds/genetic groups from varied agro-climatic zones. Milk protein genotyping was carried out in 1098 individual milk samples by SDS-PAGE at aS1-CN (CSN1S1), b-CN (CSN2), aS2-CN (CSN1S2), j-CN (CSN3), b-LG, and a-LA loci. Indian goats exhibited aS1-casein A allele in higher frequency in the majority of breeds except Ganjam and local goats. The aS1-casein A allele frequencies varied from 0.45 to 0.77. A total of 16 casein haplotypes were observed in seven breeds and breed specific haplotypes were observed with respect to geographic region. The average number of alleles was lowest in Ganjam (1.66 0.81) and highest in Sirohi goats (2.50 1.05). Expected heterozygosity at six different loci demonstrated genetic diversity and breed fragmentation. Neighbor-Joining tree was built basing on Nei’s distance. There was about 16.95% variability due to differences between breeds, indicating a strong subdivision. Principal component analysis was carried out to highlight the relationship among breeds. The variability among goat breeds was contributed by aS2-CN, b-LG and aS1-CN. The Indian goats exhibited aS1-CN (CSN1S1) A allele in higher frequency in all the breeds indicating the higher casein yield in their milk.