Plum seedlings are extensively used as rootstocks for stone fruits except P. cerasus. Genetic diversity in seedlings used for rootstocks might result in variation of scion performance and subsequently non-uniform orchards. This study aimed on investigating variation among several Iranian plum genotypes sampled from seedlings grown for grafting. Thirty-five 3- to 4-year-old seedlings were characterized using 28 quantitative and qualitative traits, as well as 22 RAPD markers. Results of the morphological study revealed remarkable variability in studied traits. Genotypes were separated into three different groups according to their height using cluster analysis performed by Ward’s clustering method based on morphological data. Twenty two RAPD primers from 120 screened produced 195 polymorphic reproducible bands (86.75% polymorphism). According to the similarity matrix, the lowest similarity was obtained between the genotype Tansgol (control) and S4-13 and the highest similarity between S11-25 and S11-26. According to the cluster analysis based on Jaccard's similarity coefficients and the UPGMA method at a similarity level of 0.56, the genotypes were divided into six sub-clusters. Significant association between eight morphological traits with RAPD markers was found by marker association analysis done using multiple linear regressions. The application of the methodology in screening elite genotypes is discussed.