The sheep is the earliest grazing animals to be domesticated that produces a great scale of animal-based protein for human consumption and plays an essential role in the modern agricultural economy. Iran is one of the important centers for sheep genetic resources and breeding in the world. The aim of the present study was to investigate the selective sweeps between three Iranian sheep breeds, namely Baluchi, Lori-Bakhtiari and Zel using the Illumina ovine SNP50k BeadChip. The Weir and Cockerham’s FST (Theta) method was applied to detect the selection sweeps across the genome. In total, thirty eight genomic regions were identified on 1, 2, 3, 4, 5, 7, 8, 10, 11, 12, 13, 15, 16, 18 and X chromosomes with high population differentiation between different Iranian sheep breed comparisons. Study of the genes has already been reported in these regions and revealed that almost all of these loci are associated with the genes involved in reproduction traits, cytology cells and nervous system, immune system, muscular system, sugar and energy metabolism. Our results reported genomic scans for selective sweeps in Iranian sheep breeds and could help detect functional candidate genes under positive selection and also better understand the relationship between genomic composition and phenotypic diversity for further genetic and breeding research in Iranian sheep breeds.