Abstract: The present study was carried out to study physical, chemical fruit properties and molecular genetic analysis between Canino cultivar and ten selected seedling apricot strains. The present survey included fruit weight, length, fruit diameter, firmness, flesh weight and flesh thickness, Total Soluble Solids (TSSs) and acidity contents in fruit juice. The results revealed that, Amar 2 (A2) had the highest average fruit weight and each of fruit length and fruit diameter were highest in Amar 1 and Amar 2, respectively. Whereas, Canino cultivar have highest fruit firmness . On the other hand, strain Amar 2 have highest flesh weight, the strain Amar 6 have highest flesh thickness and Hamawy 4 strain have highest seed weight. The TSS percentage of the Canino cultivar and apricot selected strains changed between Hamawy 1 and Amar 6. While, Hamawy 4 strain have lower acidity than others. In this study we attempted to characterize molecular genetic analysis between the ten Al-Amar selected apricot strains and Canino cultivar to detect the genetic relationship between them. Data of RAPD and ISSR analysis generated a sum of 144 bands, these bands were identified as 81 polymorphic bands out of them 19 unique bands were found to be as genotype-specific markers and considered as useful markers for apricot strains and canino cultivar. From the previous results, it can be recommended to spread these selected strains especially, Amar 1 (A1), Amar 2 (A2) and Amar 6 (A6) strains in desert land conditions and also these strains can be used in breeding programs with Canino cultivar in future according to their genetic relationship data.