The objective of the present study was to estimate the genetic diversity of wild relatives and commercial cultivars of genus Avena, using 22 random amplified polymorphic DNA (RAPD) and 10 simple sequence repeats (SSR) polymorphic markers. These two molecular marker systems were also compared for better genetic characterization of oat species. The patterns of polymorphism revealed by the two marker systems were different and level of polymorphism was higher for SSR (100 %) than RAPD (85.82 %), thus revealing SSR more efficient marker system. UPGMA cluster analysis of both RAPD and SSR data, was used to group 25 genotypes of Avena into two clusters. All commercial cultivars of Avena sativa viz., HJ-6, OS-6, Kent and HFO-114 except PLP-1 were grouped in the same cluster, depicting a narrow genetic base between the commercial cultivars. Clustering differences were also evident between SSR and RAPD derived marker systems, however, both SSR and RAPD markers grouped A. vavilovina, A. abyssinica and A. brevis into the same cluster and were distinguished from other species. Furthermore, hexaploid wild species like A. sterilis (CI 8077), A. byzantina (HFO 60) and tetraploid wild species A. insularis (HFO 865) and diploid A. strigosa (HFO 505) showed genetic divergence from cultivated species, thus may be used in wide hybridization programme for the introgression of desirable traits. The lack of diversity in oat cultivars shown in the present study demonstrates that it is urgent and imperative to enrich the north western-Himalayan oat commercial gene pool by introgression from divergent wild species.