Japanese plum (Prunus salicina Lindl.) having originated from China, is now one of the important fruit trees in many countries in the world. Knowledge of genetic diversity among existing germplasms provides the possibility of parental selection in breeding improvement programs. For assessment of genetic diversity and relationship among genotypes in Iran (Ramsar, Velyan Karaj and Mashhad) and four commercial cultivars availabe at the Research Center, Dept. Of Horticultural sciences, University of Tehran, as well as Mirobolan cultivar, eight microsatellite loci were employed. These markers produced a total of 68 bands in the studied genotypes. UDA-005 and UDP98410 loci produced the highest number of alleles (12) while CPSCT026 locus rendered the lowest (4). The average effective allele was recorded 4.1 with a maximum of 6.6 alleles at UDA-005 microsatellite site and a minimum of 2.7 at ASSR71. The average expected heterozigosity in all loci was 0.73 varying from 0.58 at ASSR71 to 0.86 at UDA-005 microsatellite locus. The average observed heterozigosity was 0.49 differing from 0.34 at UDP98410 to 0.71 at ASSR72 loci. Gene flow index (Nm) was 1.22 on the average at all loci showing the exchange of genetic material (seeds, pollen, etc.) among the locations. The mean of Polymorphic Information Content (PIC) being 0.69, indicated high heterozigosity rate among plum genotypes. Cluster analysis based on SMC similarity coefficients and UPGMA method was performed. According to clusters, groups were not in match with the geographical distribution so that genotypes with different distributions were located in same groups but there exicted certain differences between hexaploid and diploid genotypes. Based on the results of similarity matrix, the lowest and the highest genetic similarities were recorded as 0.506 and 0.92 respectively. Average similarity among genotypes recorded as 0.79, corresponding to a previous report with an average similarity whithin the same studied genotypes, using RAPD markers, (0.71).