The genes encoding milk proteins possess polymorphic forms which greatly influence the composition of raw milk and dairy products manufactured. The major milk proteins directly influencing the milk properties are whey proteins and caseins. The β-LG protein from whey fraction and κ-Casein from the casein complex are the most commonly studied milk proteins in different dairy animals worldwide. Several genetics variants of both proteins have been found associated with milk yield, total milk protein and fat contents as well as manufacturing properties of milk. Polymorphisms in β-LG and κ-casein gene CSN3 have been extensively studied in cattle; however, not much work has been reported in goats Present study was designed to identify polymorphisms in β-LG and CSN3 in Beetal and DDP goats of Pakistan and associations of identified variants with milk components were also explored. For genetic analysis, DNA was extracted from blood and quantified spectrophotometrically. The polymorphisms in β-LG were explored using PCR-RFLPs while CSN3 exon IV was sequenced and genotypes determined based on Prinzenberg et al., 2005 nomenclature. Total milk proteins and whey protein contents were estimated spectrophotometrically and casein protein contents determined. The total milk fat contents were estimated by Gerber’s method. The β-LG protein isoforms were also identified in both goat breeds through SDS-PAGE. Our results showed that β-LG AA genotype is most prevalent in both goats. The β-LG AA genotyped animals had higher total protein contents in milk while high fat contents were found in the milk of animals with BB genotype. Three β-LG protein isoforms with genotypes; AA, AB and BB were identified. The frequency of A allele protein variant was significantly higher in both goat breeds xvii while heterozygous AB genotype was the most prevalent one. However β-LG protein isoforms lacked any association with milk yield and composition. At CNS3 locus, Beetal carries A genotype whereas, DDP carried D genotype. The haplotypes revealed five polymorphisms, one silent c.245T>C whereas others were missense mutations; c.247A>G, c.309G>A, c.471G>A and c.591T>C. The CNS3 genotype A in corresponds to protein variant A and D to B. The variant protein B, prevalent in DDP goats, is found to be more economically beneficent in terms of cheese production. Daily milk yield and total milk fat contents were significantly elevated in Beetal goat. In conclusion, polymorphism exists in the β-LG and CNS3 genes as well as in β-LG protein in Beetal and DDP goats of Pakistan. At β-LG locus, A allele is dominant in both goats whereas at CNS3 locus A allele is dominant in Beetal and D in DDP. The genetic findings could be employed in future to explore suitable candidates for quality dairy products manufacture.