In the last few decades, genetic polymorphism of bovine milk protein genes such as caseins andrnwhey proteins has achieved considerable research interest mainly due to their significantrnassociations with fat and protein contents as well as the manufacturing properties of milk. In thisrnstudy, genetic polymorphisms of two bovine milk protein genes namely CSN3 and LGB werernanalyzed in five indigenous and one crossbred cattle breeds using PCR-RFLP markers andrnsequencing. Moreover, the magnitude of genetic variability within and among these cattlernpopulations at these two loci was estimated hence their population structure and phylogeneticrnrelationships characterized. For this purpose, genomic DNA was extracted from 83 animalsrnbelonging to Abigar, Boran, Guraghe, Horro, Sheko and Holestin-Barka crossbred cattlernpopulations. Both of the markers used to analyze polymorphisms in the CSN3 and LGB genesrnwere informative and enabled us to detect the widely reported CSN3-A and B and LGB-A and Brnvariants. Furthermore, sequencing revealed additional genotypes among which were the zebuspecificrnCSN3-AI and H haplotypes observed in 50% of the sequences from the indigenous cattlernand CSN3-E in one sequence derived from a Holstein-Barka crossbred cow. These CSN3rnhaplotypes were deduced analyzing a total of 7 point mutations found in the 633bp regionrnsequenced of which 5 were base transitions and 2 transversions. Two of these sites were silentrnsubstitutions while the rest were non-synonymous. At LGB locus, 12 SNPs were detected in thernamplified 529 bp region where only 3 resided in the coding region corresponding to 2 silent andrnone non-synonymous substitution. Analysis of these mutations yielded two new haplotypes (LGBBrn1 and B*) that where results of silent mutations. The PCR-RFLP assay revealed that CSN3-Arnand LGB-B were more prevalent than CSN3-B and LGB-A variants in the indigenous cattlernpopulation investigated. The frequency of allele CSN3-A (0.687) was more than twice that of Brn(0.313) where as LGB-B had a very high frequency of 0.861 compared to LGB-A (0.139). All ofrnthe breeds met HWE at both loci with the exception of Sheko that deviated significantly (P0.05) genetic differentiation among the populations studied. Most ofrnthe total genetic variation was attributed to the within population (97.23%) whereas little andrninsignificant level of variation was witnessed among the different cattle breeds (2.77%). Pairwiserngenetic distances revealed very small distances among the breeds studied. However, Shekornhad larger distances when paired with each breed where the maximum of which was with Abigarrnand the minimum that involving Guraghe indicating its relative departure from the rest.rnSimilarly, the dendrogram generated clearly depicted Sheko forming a separate branch wherernthe rest shared a second main branch.rnKey words: PCR-RFLP, Sequencing, diversity, Ethiopian cattle, SNPs, CSN3, LGB, HWE