This study was carried out to assess the genetic diversities and population structure of six camel populations of Ethiopia. Blood samples were collected from 114 camels (17-24 per population) and genotyped using10 camel microsatellite marker loci. The result revealed high genetic diversities in Ethiopian camel populations with average observed and expected heterozygosity, total number of alleles (TNA), mean number of alleles (MNA) and effective number of alleles of 0.55, 0.73,153, 6.8 (0.36) and 4.47(0.23), respectively. Among the 52 private alleles in the six Ethiopian camel populations, 31 of them were occurring at a frequency of ≥5%. It was also found that most of the variations in Ethiopian camels were attributed to within population variation (92%) while 8% was explained by between populations variation. Even though there was high heterozygosity, high inbreeding coefficient was detected in Ethiopian camel populations. From the sex camel populations 34.1, 33.4 and 28.6% alleles of Gelleb, Amibara and Liben camel populations respectively affected by inbreeding. The between population differentiation was (FST=0.11(0.01) indicating moderate population differentiation. The neighbor-joining tree and structure analysis show that the Ethiopian camel populations were clustered into four subgroups. The Afar camels were grouped into two together with the Ethiopian Somali camels (Jigjiga with Mille and Gelleb with Amibara) and the two Ogaden camels (Liben and Hoor) are separated into two subgroups indicating that some of the Afar and the Somali camels were admixed. Therefore, even though high hetrozygosity within population and moderate genetic differentiation between populations were observed, the presence of high inbreeding coefficient may affect hetrozygosity in the overall populations.
