Myrtle) Myrtus communis L. (is one of the most important medicinal plants because of its application in pharmaceutical and food industries. In this study, morphological, molecular markers and essential oil content were applied to evaluate the diversity of Iranian myrtle populations. High variation was obtained in respect to essential oil content and morphological traits among populations. Essential oil content ranged from 1.06% in Chaharmahal and Bakhtiari (sw.ch.o) to 2.28% in Lorestan (w.l.d). Eight SRAP primer combinations were also used to examine the genetic diversity of 86 accessions belonging to the 11 myrtle populations, 440 bands were generated that created the polymorphism was 99.79 %. The seven ISSR markers used amplified 292 bands, resulting in a polymorphism of 99.25%. The PIC values for SRAP marker were 0.42 and for ISSR marker was 0.40, which indicates high polymorphism in the studied populations. Cluster analysis of 11 Myrtle populations using the Jaccard method and the UPGMA algorithm delineated the accessions into five groups, although the grouping did not fit perfectly with the geographic regions. The genetic similarity coefficients calculated using the Jaccard similarity coefficient showed ranged from 0.03 to 0.93, indicating a wide range of genetic variations among the studied populations. The results of principal coordinate analysis (PcoA) were in line with the results of cluster analysis. The first five component in SRAP marker, and first five components in SRAP-ISSR markers were able to justify 69.83% and 71.85% of the total variation among the accessions. In terms of distribution among and within populations, the greatest similarity was found between the populations of the Chaharmahal and Bakhtiari-Madan (sw.ch.m.), and Chaharmahal and Bakhtiari-Anjo (sw.ch.a) (0.939), and lowest among the populations of the Chaharmahal and Bakhtiari-Madan (sw.ch.m) and Fars-Nourabad (s.nor) (0.743). Also, the highest genetic distance was observed between the populations Fars-Nourabad (s.nor) and Chaharmahal and Bakhtiari-Madan (sw.ch.m) (0.296), and the lowest genetic distance was observed between Chaharmahal and Bakhtiari-Madan (sw.ch.m) and Chaharmahal and Bakhtiari-Anjo (sw.ch.a) (0.062). According to analysis of molecular variance (AMOVA) 89.31 % of total variation was associated to within and 10.69 % of variation was observed among populations. Relatively high genetic differentiation (Gst = 0.31) and gene flow (Nm = 1.11) was observed among populations. W.l.c.m population from Lorestan revealed the highest values of number of observed alleles (Na), number of effective alleles (Ne), genetic variation (H), Shannon index (I), and the percentage of polymorphic loci (PPL%). The results of population structure analysis revealed high admixture of myrtle accessions in the populations. Finally, SW.ch.m from Chaharmahal and S.nor from Fars revealed the highest genetic distance as well as high essential oil content that might be suggested for further breeding programs in myrtle. Key words : Myrtle, Genetic Variation, Essential oil, Morphology, SRAP, ISSR