The genetic structure of 10 goat breeds from four countries of the Middle East and Horn of Africa was investigated at 17 microsatellite loci. The average allele number and richness were 9.65 and 5.78, respectively. The mean expected heterozygosity per population was 0.703, 0.715, 0.719, 0.699, 0.749, 0.719, 0.731, 0.721, 0.719, and 0.730 for Somali from Somalia, Tohami, Bishi, Jabali, Ardi, and Saudi Damascus from Saudi Arabia, Black Bedouin, Sahrawi, and Jordanian Damascus from Jordan, and Syrian Damascus from Syria. The low level of genetic differentiation across large topographic features was expressed by pairwise difference coefficient (FST = 0.001-0.135). The goats were assigned to four genetic pools, indicating the occurrence of gene flow within a potential genetic exchange network. The genetic exchange possibly occurred in the past when the ancient trade routes - Incense and Pilgrimage Routes - were active in these countries. Despite the distances far by thousands of kilometers or separated by the boundaries, Saudi goats kept a reasonable level of admixture, indicating common ancestry. These results are in agreement with a known history of the goat populations in regards to geographical location and evolutionary time of past common ancestors. Further study is recommended considering goats from other Middle East countries.