Prunus microcarpa Boiss. is well adapted to severe winter and dry-hot summer conditions, and may have the potential of being a dwarfing rootstock that provides precocious bearing, or could be used as a valuable new source of germplasm. In the present investigation, a total of 100 accessions of this species were evaluated using 27 phenotypic characteristics. The analysis of variance outcomes showed significantly different morphological characters among all the studied accessions. Petal length varied from 2.77 to 7.85 mm, while petal width ranged from 1.86 to 6.26 mm. In addition, leaf length ranged from 4.71 to 13.31 mm, while leaf width varied from 2.95 to 8.50 mm. Fruit length ranged from 3.70 to 10.47mm and fruit width varied from 1.94 to 9.64 mm. Fruit weight ranged from 0.17 to 0.90 g, while stone weight varied from 0.06 to 0.19 g. Leaf length was positively correlated with fruit length (r=0.22) and fruit weight (r=0.28). Principal component analysis (PCA) could describe the evaluated traits as seven main and independent components which were able to justify 72.09% of total variance. The studied populations were placed into three groups, indicating a high phenotypic diversity among and within them. Finally, P. microcarpa can be considered as characterizing the large gene pool that contributed to the domestication process of cherries. Furthermore, the conservation of the highly diverse native populations of this wild species should be mainly considered.