The present work aimed at study genetic diversity and the sources of molecular variation between the individual cloves of two garlic clones with different molecular markers, RAPD and SSR. Three bulbs of two garlic clones (Egaseed1 and Balady) were germinated (three individual cloves of each bulb). The total genomic DNA was extracted from the young leaves. Ten RAPD and fifteen SSR primers were used and the data were statistically analyzed. Fifty-seven bands (including 4 unique and 53 polymorphic) were totally generated and there were no monomorphic bands from ten RAPD primers. Similarly, no unique bands were generated by seven primers, whereas other produced only one unique band of 433 and 417 bp, respectively. Two unique bands of 124 and 188 bp were detected with K10 RAPD primer in Egaseed1 clone. Twelve SSR primers produced 45 DNA fragments. Out of them, 12 were monomorphic and the remaining were polymorphic. Different molecular markers could be used to evaluate genetic diversity and confirm the molecular differences between the cloves derived from the same bulb and the differentiated nature of garlic. In addition, it defines the importance of using molecular markers to evaluate different garlic clones.