Abstract The genetic diversity of most global goat populations has been assessed in recent decades using nuclear markers but remains unstudied in the south Arabian Peninsula, particularly in the Sultanate of Oman, despite the importance of these animals for the local economy and food supply. Therefore, the present study provides a comparative analysis of the genetic diversity of five native Omani goat populations and evaluates possible admixture rates with the four most frequently imported goat populations from geographically proximal countries. A dataset based on 11 highly informative microsatellite locus genotypes from nine populations was used to estimate population genetic parameters. The summary statistics for the parameters depicted relatively highly diverse populations (Ho = 0.667, He = 0.663) with relatively low and mostly non-significant levels of inbreeding (FIS). Furthermore, population substructure estimators (AMOVA) and population differentiation coefficient (FST) indicated weak genetic differentiation among populations (P

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