Genetic diversity of goat breeds in Jordan was investigated using six microsatellite markers (MS). The markers were BM143, CSRD247, INRA40, OARAE54, ILSTS005 and MCM527. The selected goats were predefined into four breeds based on morphological and geographical considerations as Jabali, Dhaiwi, Shami and Sahrawi. The number of alleles, expected and observed heterozygosity per population and locus were (6.92, 0.703, 0.685, and 9.83, 0.728, 0.624, respectively). The average population differentiation coefficient (Fst) and inbreeding coefficient (Fis) were 0.019 and 0.048, respectively, indicating greater differentiation between pairwise breed comparisons and more inbreeding found in each breed than expected. In particular, Fis values were 0.064, -0.020, -0.070 and 0.123 in Jabali, Dhaiwi, Shami and Sahrawi, respectively. The Fst values were largest (0.078) between Shami and Sahrawi, and smallest (0.024) between Jabali and Dhaiwi. These results reflected high level of genetic diversity and differentiation in studied goat breeds as well as at the studied markers. On the other hand, genetic distances undoubtedly confirmed breed differentiation among the studied goat breeds. Distance matrix was constructed of four taxa representing the four breeds. Our current findings showed closeness of Dhaiwi to both Jabali and Sahrawi. Those three breeds were clustered together, whereas Shami was in a separate cluster. The population structure analysis inferred that four breeds would form the four predefined breeds. As a consequence, individual correspondence analysis confirmed the degree of differentiation between all individuals of the four studied goat breeds except only few individuals of Sahrawi goats that may have descended from other breeds of nearby countries. The present study provides the first microsatellite genetic diversity and differentiation of goat breeds in Jordan.