Genetic variability is a prerequisite for any plant breeding program. Using diverse plum resources to broaden the genetic base worldwide and improving local cultivars for the development of the plum industry are important objectives for breeders. In this study, the molecular, morphological, and pomological characteristics of Prunus domestica L., naturally growing in the East Mediterranean region of Türkiye, were investigated. To identify phenotypic variation within this species, 44 variables were recorded over two years (2023 and 2024) for 100 accessions. The highest coefficient of variation was observed for the presence of thorn at 194.93%. Fruit weight ranged from 5.56 (G18) to 29.79 g (G30), fruit width from 19.79 (G8) to 36.80 mm (G44), fruit length from 19.01 (G30) to 37.56 mm (G18), leaf length from 28.39 (G79) to 62.90 mm (G39), and leaf width from 11.56 (G87) to 40.84 mm (G17). Principal component analysis revealed that the first 20 principal components explained 77.04% of the total variation. The dendrogram created using Ward’s method and Euclidean distance divided the accessions into two groups. Group B exhibited high variation in terms of morphology and pomology, with 99 accessions. Twenty accessions (G53, G26, G2, G90, G44, G78, G89, G55, G17, G52, G28, G11, G14, G85, G66, G38, G21, G98, G67, and G32) were identified for their superior fruit quality and yield characteristics. To assess the molecular genetic diversity of the plants, eight different inter simple sequence repeats (ISSR) primers were utilized, resulting in a total of 104 scorable bands. Among the bands obtained, 98 were found to be polymorphic. A total of 98 bands were polymorphic, and the polymorphism rate was 94.38%. As a result of the molecular analysis, the similarity index in the dendrogram of the cluster analysis using the unweighted pair group method with arithmetic mean (UPGMA) ranged from 0.55 to 1.00. G65 and G79 accessions were determined to be genetically closest with a similarity index of 1. The results of this investigation underscore the importance of preserving this invaluable genetic resource both in its natural habitats in the Eastern Mediterranean Region of Türkiye and ex-situ in germplasm
