Analysis of molecular variance using (AMOVA) was conducted using 1023 permutation settings for all 13 RM Y-STRs in Arlequin [[8]Excoffier L. Lischer H.E.L. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows.]. In order to further exemplify the results, both pairwise FST and linearized Slatkin’s pairwise FST resulted were plotted as matrix using R software package incorporated within Arlequin software v3.5. The genetic structure of the Qatar populations was evaluated by calculating the FST value for the total population and pairwise FST comparisons between them. Also, the comparison was performed to the other Gulf countries of (Qatar, Middle East, Kuwait, KSA, Bahrain, UAE and Yemen) when compared to the worldwide data set. The result of pairwise FST is significant which indicate that the haplotype frequencies are different between populations. Gulf countries published data were grouped as on group region since they are all located in close geographic region after the analysis between Qatar and worldwide data. They were grouped since they are in one region in the Middle East and compared to the published Middle East data (Turkey). The results show the following values: The pairwise FST between Qatar and UAE was (FST = 0.00957); between Qatar and Bahrain, it was (FST = 0.01037); between the Qatar and KSA populations; the medium FST value between Qatar and Yemen was (FST = 0.01723); between Qatar and Middle East was (FST = −0.01059) and finally the average pairwise FST was (FST = 0.00648). The average FST value between Qatar, gulf countries and Middle Eastern population was (FST = 0.01387). Overall, the majority of the resulted pairwise FST values are less than 0.2 which also indicate a very low substructure between populations as mentioned previously [[4]Ballantyne K.N. Ralf A. Aboukhalid R. Achakzai N.M. Anjos M.J. Ayub et al.Toward male individualization with rapidly mutating y-chromosomal short tandem repeats.].