The two Ethiopian chicken populations, Horro and Jarso, show genetic divergence likely due to limited gene flow, different demographic histories, and management under different ecological conditions. Horro chickens show less genetic diversity than Jarso chickens. Analysis of single nucleotide polymorphisms found significant genetic differentiation between the two populations, with 28% of genetic variation explained between populations. The results indicate the populations descended from different ancestral origins and developed independently under different environmental and management conditions.