The African Horn region that includes the Abyssinian is one of the areas in the world that harbor high human genetic diversity manifesting past intermingling of people of different origins attributed to its geographic immediacy to the middle east and being historical trade and religio-cultural hub. Here, we performed a genetic structure analysis of linguistically differentiated populations of Ethiopia, South Sudan, and Somali. To get insight into the genetic landscape of the horn of Africa vs the rest of the world, we leverage HapMap SNPs data from Utah residents with Northern and Western European ancestry (CEU), Maasai (MKK), and Yoruba (YRI) and analyzed for genetic admixture and diversity. The genetic and linguistic affiliations mismatch for most Cushitic and Semitic language speakers. The gradients of genetic variations among the different sub-populations within the region show gene-flow directions and past mass population movements. Ethiopians that predominately inhabited the central and northern Ethiopia harbored ~10-15% of CEU admixture. The total African horn ancestral line contributed ~20%, 5%, and 2% to MKK, YRI, and CEU, respectively. MKK showed a high genetic diversity comparable to the Ethiopian Cushitic, Semitic, and North Omotic language speakers. Allelic distribution frequencies among the populations at some outlier loci may also provide insight into the adaptations to critical environmental factors such as Malaria. Key words: Horn of Africa, Ethiopia, ancestry, genetic structure, linguistic variation, haplotype, adaptive loci, geneflow