Linseed is an important Rabi season oilseed crop next to rapeseed and mustard in terms of area and production. During the last two decades, flax has attracted great attention to human health mostly because of its desirable fatty acid composition. Genetic variability is crucial in the breeding or selection program of any crop. The success of any genetic program lies in exploiting genetic variability. Diversity analysis of flax is an important component for efficient management and utilization of its genetic resources, and proper handling of the seed certification programs. The present research work the linseed genotypes and understanding its diversity on both morphological and molecular levels and understanding the properties of the linseed. Based on divergence analysis, the genotypes viz., SLS 108, PKDL-167, SLS 111, JLS 67, SLS 123, SLS 118 and TL142 were identified as promising genotypes indicating vast genetic divergence regarding cluster means, intra and inter-cluster distance and per se performances. At the molecular level, twelve SSR markers were found polymorphic. The polymorphic information content (PIC) values were ranged between 0.0555 to 0.6732 with an average PIC value of 0.4020 per primer. This depicted that there is considerable genetic variability amongst the genotypes used in the molecular study and also, this was similar to the results of D2 analysis done based on quantitative data. Unique allele was found for marker Lu-1, Lu-4, Lu-7 and Lu-8 in genotypes JLS-9, PKDL-167, SLS-16 and SLS-115 and the size was about 90 bp, 800 bp, 170 bp and 220 bp, respectively. These markers can be used for selective amplification and identification of the above specific trait/genotypes.