Selection for increasing of frequency in new mutations that are advantageous only in a subset of POPULATIONs leaves some signatures in the genome. Detecting these genomic regions is one of the most important areas of research in animal genetics since locations of selection signatures are often correlated with QTLs affecting economically important traits. In this paper, a whole genome scan using ~54000 SNP markers was performed in two main Iranian sheep breeds, namely Zel and Lori-Baktiari, with the aim of identifying divergently selected regions of the genome. Study of POPULATION DIFFERENTIATION across the genome using Weir and Cockerham’s FST test revealed some regions showing evidence of selection. In this paper, five regions which were in the 99.99 percentile of the genome distribution of FST scores were selected for further analysis.These regions were located in chromosomes 2, 5, 7 (two areas) and X. To evaluate the selection sweep, due to linkage disequilibrium, associated with these signatures we employed the Extended Haplotype Homozygosity (EHH) test. The results of this test as well as a study of haplotype bifurcation diagrams in these breeds also confirmed large allele DIFFERENTIATION in these regions.Finally, study of reported QTL regions in the orthologous areas of the cattle genome showed that they overlapped with the reported cattle QTLs, representing economically important traits such as carcass yield and reproductive traits. In conclusion, the results from this study provide one of the first attempts to develop a genome-wide map of selection footprints in the sheep genome and may facilitate the identification of genes affecting traits which are divergent in these two Iranian sheep breeds.