Mukhongo et al, 2014/J. Livestock Sci. 5: 65-78 65 Genetic Diversity and Population Structure of the Indigenous Sheep in Kenya Based on Microsatellite Analysis: Implications for their Conservation D. M. Mukhongo 1* , O Mwai 3 , M Tapio 4 , A. Muigai 2 , 1- University of Cambridge, UK, 2-Jomo Kenyatta University of Agriculture and Technology-Nairobi, Kenya , 3-International Livestock Research Institute-Nairobi, Kenya, 4- MTT Agrifood Research Finland, 31600 Jokioinen, Finland * Corresponding author & address Leverhulme Centre for Human Evolutionary Studies University of Cambridge Fitzwilliam Street, Cambridge CB2 1QH Contact email address:denmismuk@gmail.com Journal of Livestock Science (ISSN online 2277-6214) 5:65-78 Received on 25/06/2014; Accepted on 20 /07/2014 ABSTRACT Knowledge of the genetic relationship and admixture among neighbouring livestock populations is crucial for conservation efforts. This study analyzed the molecular diversity of fifteen sheep populations (both indigenous and exotic) in Kenya. Blood samples from 582 individuals were genotyped across the 15 microsatellite markers. The expected heterozygosity and Mean number of alleles ranged from 0.596 to 0.807 and 6.67 to 9.33 respectively. Most populations showed significant heterozygote deficiency due to a moderately high level of inbreeding, f IS (0.109). Population genetic differentiation was reasonably high (θ ST = 0.101). Four population clusters majorly based on geographical proximity and interbreeding among populations were detected. These results indicate levels of admixture warranting institution of conservation measures. However, a more encompassing study including all regions in the country as well as more microsatellite markers is necessary to comprehensively understand the dynamics of genetic introgression. Keywords: Admixture; exotic breeds; gene flow; Sustainable breeding programs