The current study was carried out at Rice Biotechnology Lab, RRTC, during 2016-2017G to estimate the genetic diversity of eleven commercial rice varieties at the molecular level. Sixteen sequence-related amplified polymorphism (SRAP) and Eighteen Inter-Simple sequence repeats (ISSR) were used to access the molecular diversity. The studied varieties included 7 pure Japonica, 2 pure Indica and 2 Indica Japonica varieties. SRAP primers generated a total of 579 bands with average of 36.19 bands/primer pair across tested genotypes. The number of amplified genetic loci (alleles) ranged from 4 to 8 with a total of 85 alleles across all tested primers. The polymorphic alleles ranged from 3 in ME6xEM4 to 7 alleles in ME4 x EM7 and ME8 x EM8 primer combinations. The PIC values ranged from 0.645 to 0.859 with overall PIC value of 0.776. UPGMA-based clustering of the eleven commercial varieties separated the studied varieties according to their genetic background. The pure Japonica group, Pure Indica group and the Indica/Japonica group. The eighteen ISSR primers generated 897 amplified bands with average of 49.72 bands/primer. A total of 132 alleles were assessed that ranged from 4 alleles in ISSR11 and ISSR13 to 12 alleles in ISSR18. The overall PIC value was higher than that of SRAP primers and recorded 0.830. Although ISSR system successfully separated the three different groups, the subgroups arrangement on the dendrogram varied. The results showed the existence of considerable amount of molecular diversity among commercial varieties. Both marker systems showed high resolution power in assessing diversity, however, SRAP results were more aligned with varietal genetic background. The study suggests also the possible reliance on molecular marker systems in assessing genetic diversity.