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The ability to adapt to harsh environments and thrive with minimal food and water input, places goats among the most popular livestock species in Arab countries. However, little is known about the historical and contemporary genetics of most Arabian goat breeds and populations. In this study, we genetically analyzed 617 individuals (126 from this study and 491 from published sources) representing 18 Arabian goat populations by evaluating variation in the mitochondrial DNA control region (D-loop). Our data were also combined and compared with those from 339 Asian, African, European and Canarian populations. We found 186 different polymorphic sites, which allowed us to identify 453 different haplotypes belonging to three maternal haplogroups: A, B and G. Haplogroup A is the most represented among Arabian goats and highly widespread among Arab countries, whereas B group is rare. Haplogroup G is the second most frequent haplogroup and also the most diverse among Arabian goats. Measurements of nucleotide and haplotype diversity and the mean number of pairwise differences in the 18 populations yielded values of 0.025, 0.998 and 10.586, respectively. These results show that the diversity of native Arabian goat populations is high and similar to that of populations at the center of origin. Based on estimated population structures, comparison of pairwise F ST and AMOVA values between Arabian populations indicated low genetic differentiation. In addition, median-joining network analysis results provide very little evidence of a previous connection between Arabian goats and regions of historical Arab influence were once installed (Iberian Peninsula and Southern Europe). Finally, the same thin evidence was also found between extant Arabian and Canarian goats, which might have partially originated due to commercial trade or during the migratory movements of ancient humans.