The aim of the present study was to estimate the molecular characteristics, structure, genetic diversity and genetic bottlenecks in the three sheep populations native to Iraq (Awassi, Naaimi, and Arabi). For this purpose, 12 microsatellite loci with chromosomal distribution distributions (1, 2, 5, 9 and 14) were used according to the recommendations of FAO and the International Society for Animal Genetics (ISAG). Sixty samples of whole animal blood (both sex) were randomly collected from the relevant populations in Karbala, Najaf and Babel provinces. The genomic DNA extraction, quality and quantity, preparation of PCR, electrophoresis photography was done accordingly based on standard available methods. After observation of raw genotype per investigated loci, allele binning was done for minimizing genotyping errors. More than 9 types of molecular statistical indices (allele frequencies, observed and effective number of alleles, observed and expected heterozygosity, PIC, Wright coefficient, Shannon index, F-statistical indices, genetic distance and the bottleneck) Checked out. The results were presented in two parts: evaluation of microsatellite loci utility and evaluation of genetic diversity within and between the population. The results of the first part showed that the highest polymorphism was observed in OarFCB226 and TGLA13 markers and the rest had the lowest polymorphism. The results of the second part showed that the Awaasi and Arabi breed have the highest and lowest diversity, respectively. The highest genetic distance was between Arabi and Naaimi breeds and the smallest was between Naaimi and Awassi breeds. Furthermore, bottleneck L-Shape curve showed that the studied populations are in a genetic predicament.