The genetic diversity between livestock is an important indicator for experts and researchers in the field of livestock management. It assists them to design breeding programs, improve quality and enhance productivity of the livestock. Subsequently this leads to raising the efficiency of its genetic origins as well as preserving it from genetic drift. The present study is the first of its kind that characterizes genotypic variability of Oman goat populations. In this study the genetic diversity in Omani goat breeds was investigated based on microsatellite DNA loci. Five native Omani goat breeds (Batina, Musandam, Dhofari, Al Jabal Al Akhdar and Sharqiyah) and two exotic goat breeds (Iranian and Somali) were studied. Blood samples were collected from 202 unrelated animals and the genomic DNA was extracted using QIAamp Blood Midi Kit. The 10 microsatellite markers (recommended by the ISAG/FAO) were amplified by PCR using specific protocols. PCR products were run on Agarose gel mixed with Ethidium Bromid then visualized under UV light. The microsatellite alleles were sized using 100 bp DNA ladder. Fragment analysis was carried on ABI Prism genetic analyzer 3130. Microsatellite fragment sizing was performed using the GeneMapper® and Allele calling was performed with the software and were manually checked to avoid false calling of alleles. A total of 161 alleles were detected across the seven goat breeds. The number of alleles detected per locus varied from 9 to 23, with an average of 16.1 alleles per locus. The mean number of alleles of Omani breeds was 9.02 with the range between 7.7 (Batinah and Sharqiyah goat) and 11.6 (Musandam goat). The mean number in Iranian and Somali breeds was lower than for Omani goat breeds (8 and 6.6, respectively). The mean observed and expected heterozygosity values across all loci for all populations were 0.602 and 0.707, respectively. The mean value of PIC and effective number of alleles were 0.677 and 8.53, respectively. The mean number of migrants between populations per generation (gene flow= Nm) across all breeds was 3.69. Genetic distance was least (0.130) Sharqiyah and Jabal Akhdar and highest between Jabal Akhdar and Somali breeds (0.478).. Deviations from HW proportions were extenuated for the studied microsatellite loci for all populations. Significant linkage disequilibrium (P<0.05) was detected in 34 locus pairs out of 315 pairs. The coefficient of gene differentiation (Fst), within breeds (inbreeding) (Fis) and inbreeding for all population (Fil) were 0.08, 0.158 and 0.222, respectively. AMOVA results revealed higher genetic diversity within populations compared to diversity among them. A genetic distance matrix used to assess the genetic relatedness between goat populations. An UPGMA cluster and PCoA analysis indicates that microsatellite markers were effective indistinguishing between goat breeds and useful in differentiations between closely morphological related goat breeds. This study showed that the primers used are suitable for the genetic characterization of native Omani goats. Traditional management systems might have been playing a role in the diversity detected in most of Omani goat populations. Thus the conservation strategies of the local goat breeds should be considered in the near future. Findings of the current study may be used as tools to establish national conservation and breeding towards important economic traits.