The most common factors affecting somaclonal variation are genotype, explants source, in vitro period and cultivation conditions.Genetic stability of two Iranian olive cultivars (Mari and Rowghani)microshoots were evaluated inthree different concentrations of copper( 0.5, 1, 1.5 μM) during four culturing period. Genetic modification from desiccation, were investigated at the DNA level using SSR method. In vitro shoots were screened by 6 microsatellite markers. In total, 14 alleles were detected with a mean number of 2.33 alleles per locus. The phenogram obtained by UPGMA clusteringshowed variability between two cultivars but it revealed at different Cu concentrations and culturing period,themicropropagated plants of each cultivar were genetically stable and similar to the maternal plant.