This investigation was carried out for two successive seasons (2021 and 2022) on Solitaire and Charisma apricot cultivars four years old trees budded on Nemguard Rootstock grown in sandy soil at private orchard, in Assiut  governorate, Egypt to evaluate the vegetative, flowering, yield, fruit characters and Molecular Genetic Markers. Data showed that Solitaire was superior than Charisma in total opening number of flower buds, yield in kg/tree, fruit and flesh weight, while shoot length, vegetative bud number, trunk circumference, fruit firmness and harvesting period were longer in Charisma during two studied seasons. The Molecular genetic evaluations were determined by using SCoT and ISSR molecular analysis for PCR reactions. Results revealed a sum of 43 band and these bands were identified as 28 monomorphic and 15 polymorphic ones with polymorphic % (34.88 %) and the polymorphic bands were scored as 18 specific markers, only six of them were positive markers were detected with both of Charisma and Solitaire cvs. By the way, there were genetic variation between both cultivars and also, data were obtained specific markers for each cultivar may be linked to specific traits for each cultivar and this results would be more useful for crop improvement programs. On the other hand, Heterostyly phenomenon for Solitaire cv. was observed during the flower study so, this cultivar needs to cultivar with another apricot cv. blooms at the same time or spread beehives for cross pollination to solve this problem. Finally, we can recommended with spreading of these cultivars under Egyptian conditions.