Plum (Prunus salicina L.) includes more than 20 species with morphological variations, a wide genetic variety and nutrient qualities that are beneficial to human health. The properties of plum fruit cultivars that are influenced by their genetic profile can be used for effective evaluation. In order to identify chemical constituents and genetic relations among ten plum cultivars grown in Egypt, studies were carried out on the chlorophyll in leaves, some physiological characteristics of fruits, chloroplast (cpDNA) and mitochondrial DNA (mtDNA). Significant differences were observed in chlorophyll a, chlorophyll b and carotenoids in plum leaves, as well as total sugar, total soluble solids (TSS), pH and titratable acidity (TA) among plum cultivars. Five cpDNA regions (trnL, trnL- trnF, trnH-psbA, matK and rbcL) and two mtDNA regions (nad4 and nad9) were amplified. Among the loci, the PCR success rate varied greatly; the locus nad4 in the mitochondria had the greatest success rate 100 % followed by the chloroplast loci rbcL and matK 60%, then (trn L, trnL- trnF, trnH- psbA and nad9) with a success amplified rate of 50%. This study supports the applicability of the cpDNA and mtDNA markers to detect and identify the cytoplasmic variation in plum trees. The study will contribute to the knowledge about Prunus salicina cultivars and will be helpful in expanding the plum gene pool, which can be utilized in future plant breeding programs for the improvement of existing plum cultivars.