Introduction: Horse has been of great interest to humans due to its speed, strength, and endurance. Based on its role in human history and civilization, it is considered the most important domesticated animal. Iranian horse breeds are bred in the north, south, and west regions of the country. Arabian horse is one of the international breeds in the world, which is bred in more than 60 countries. Preliminary evidence shows that the Arabian horse breed was established about 3000 years ago and was bred in small populations in many countries of the Middle East, including Egypt, Iran, Saudi Arabia, and Syria. These separate populations have led to the development of different maternal strains of the Arabian horse. Genetic diversity is necessary for genetic conservation and survival of the breeds. Molecular markers are used to assess the structure and genetic diversity of different populations. Therefore, one of the suitable markers is a microsatellite. Regarding the importance of genetic diversity in the survival of the breed, and designing the genetic conservation and breeding programs, the purpose of this study was to investigate the population structure and genetic diversity of Arabian horse breeds using microsatellite markers. Materials and Methods: In this study, hair root samples were obtained from 8673 (5602 mares and 3071 stallions) Arabian horses from Khuzestan, Yazd, Kerman, Isfahan, Lorestan, and Alborz provinces. DNA samples were extracted from hair roots using the Direct PCR Kit (Thermo Fisher Scientific, Vilnius, Lithuania). The quantity and quality of the extracted DNA were controlled by spectrophotometry and agarose gel methods. The number of 10 microsatellite markers including AHT04, AHT05, ASB02, ASB17, ASB23, HMS03, HMS06, HMS07, HTG10, and VHL20 were used based on ISAG recommendation. Then, the amplification of genomic fragments and the genotype of samples was determined by COrDIS Horse Reagent Kit (Moscow, Russia). Forward primers were labeled with fluorescent dye at 5'-end. These microsatellite loci were amplified by the multiplex PCR method. Then, the PCR products were genotyped by the Genetic Analyzer system and the capillary electrophoresis method. Obtained data were used to estimate demographic parameters. The number of effective alleles, the number of observed alleles, the observed heterozygosity, the expected heterozygosity, and the Shannon index were calculated by GenAlex 6.5 software. Genpop 4.7.5 software was used to calculate the FIS statistic or Fixation index in the population. Results and discussion: The results showed that the lowest and highest number of observed alleles were related to ASB17 (17 alleles), HMS06 (eight alleles), and HMS07 (eight alleles) markers, respectively. The total number of alleles observed at all loci was 113 alleles. The average number of observed alleles was estimated to be 11.3, which indicates high allelic diversity in the Persian Arabian horse. The mean number of effective alleles, Shannon index, observed and expected heterozygosity and Fixation index were 3.97, 1.58, 0.721, 0.736, and 0.021, respectively. The mean genetic diversity in the Arabian horse's population was calculated to be 0.736. The highest and lowest genetic diversity was observed in VHL20 (0.803) and ASB02 (0.620) markers, respectively. The average number of effective alleles per locus in studies conducted in different countries on Arabian horses, including Egypt, Syria, and Western countries, with Persian Arabian horses in this research, showed that number of effective alleles is higher in Persian Arabian horses. The average Shannon's index has been reported to be slightly lower in previous studies of Persian Arabian horses, which is probably due to the small number of samples in these studies compared to the present study. The highest and lowest observed heterozygosities in this study were related to AHT4 (0.788) and ASB02 (0.613) markers, which were consistent with the results of the research conducted on Arabian horses of Iran, Syria, and Egypt. The positive FIS value in Arabian horses made a decrease in heterozygosity in the population, an increase in homozygosity and consequently inbreeding in Arabian horse populations. In this research, all studied loci showed a significant deviation from the Hardy-Weinberg equilibrium. Except for the AHT04 marker, which deviated from the Hardy-Weinberg equilibrium at P<0.01, the others have deviated at P<0.001. Deviation from the Hardy-Weinberg equilibrium can indicate the presence of some factors disturbing Hardy-Weinberg equilibrium, such as migration and selection, which in Persian Arabian horses, the entry of stallions from outside the herd and the gene flow between different maternal strains and also the existence of a selection program among breeders are the main factors of deviation from Hari-Weinberg equilibrium. Conclusions: Evaluation of the genetic structure of Arabian horses of Iran and comparison with other Arabian horses in the world, including those in the Middle East region, showed that Arabian horses of Iran have a higher genetic diversity, which is probably due to the presence of different maternal strains in Iran, high gene flow among the different strains, a large import of Arabian horses and crossbreeding with Arabian horses of Iran, as well as a high number of samples and so identification of new alleles in this research. On the other hand, the rate of inbreeding was positive according to the FIS in Iran Arabian horses, indicating a risk of genetic diversity loss and increasing inbreeding in these horses. Therefore, management of genetic diversity and prevention of mating among related animals should be considered. [ABSTRACT FROM AUTHOR]