Understanding the pattern of linkage disequilibrium (LD) in different populations provides useful information for genomic selection (GS), genome wide association studies (GWAS) and identification of genetic architecture of traits by estimating the persistence of LD phase between markers and quantitative trait loci (QTL). The aim of this research was to estimate of the extent of LD in three Iranian native sheep breeds. Therefore, 186 blood samples were taken from three sheep breeds (96 Baluchi, 45 lori-Bakhtiari and 45 Zel) and genotyped by Illumina ovine 50K SNPChip, then linkage disequilibrium in any breed were measured using r2. The results showed that the highest average values of r2 at inter marker distance of less than 10Kb were 0.392± 0.323, 0.360±0.308 and 0.340±0.306 in Baluchi, Lori-Bakhtiari and Zel, respectively. The highest average values of r2 in autosome chromosomes of each breed were obtained for chromosome 24 and 25 in Baluchi, 9 and 21 in Lori-Bakhtiari and 23 and 24 in Zel. The amount of LD reduced with increasing the distance between markers, the extent of LD was less than 0.1 at inter marker distances greater than 100Kb. The comparison of correlation coefficients LD between different breeds showed a strong persistence of LD phase between Zel and Lori-Bakhtiari breeds which is probably due to recent common ancestors between these two breeds. Generally, with increase amount of LD means that lower marker density in association studies will be required. The results of this study showed to achieve genomic prediction accuracy of 85% (assuming there is no other accuracy limiting factor) and robust GWAS results, the density of markers must be higher than 50K SNPChip.