The immune systems of species are basically dynamic for evolution and survival, and the animal selection patterns in innate immune loci are of prodigious importance in molecular evolutionary research. Interferon alpha (IFN-α) plays a fundamental role in innate immune response with biological and antiviral activity. In the current study, the IFN-α gene was genetically and phylogenetically characterized in thirty Beetal goats by direct sequencing. Genomic DNA was isolated and sequencing analysis of IFN-α gene revealed two missense substitutions (A83G: Lys28Arg, A127G: Thr43Ala) and one synonymous substitution (A144G). Phylogenetic analysis and genetic distance showed the species-wise clustering and higher genetic distance with other goats. This information in Pakistani indigenous goats may provide useful insights into the design of molecular selection strategies for genetic improvement of animal and further biological studies in other goat breeds may provide evolutionary way to acquire better disease resistant animals.