Knowledge of the genetic diversity and structure of tree species across their geographical ranges is essential for sustainable use and management. Prunus scoparia (Spach) is a wild almond species native to Iran. It is naturally widespread as a forest resource in many regions of Iran. In the present study, the phenotypic diversity of 198 accessions of this species was evaluated using morphological characters. Significant phenotypic diversity was detected among the studied accessions based on morphological traits. Simple correlation coefficient analysis showed the existence of significant positive and negative correlations among characteristics. The majority of significant correlation coefficients were to be found between the characteristics representing nut and kernel sizes. Principal component analysis showed that 73.37% of the phenotypic variability was explained by all of traits for the studied accessions where green fruit dimensions, nut dimensions, nut weight, shell weight, kernel dimensions and kernel weight contributed most of the total variation. Cluster analysis confirmed considerable variation in the studied germplasm and identified two major clusters with several sub-clusters. P. scoparia shows great tolerance to abiotic stresses such as drought, salinity, low soil fertility and low winter temperatures; therefore it may present an important genetic resource to be used in breeding programs and/or directly as a rootstock for almond that is more adapted to climate change. The present results provide important new information for gene pool conservation and screening for superior germplasm and breeding.