Abstract: Saffron derived from Crocus sativus is the most expensive, flavored and colorful spice with worldwide importance and utilities in many disease conditions. Many efforts have been made to detect variability in this plant. We used sequence specific amplified polymorphism (SSAP) and retrotransposon microsatellite amplified polymorphism (REMAP) markers for analyzing the genetic diversity among thirty accessions of Crocus sativus. Besides, we also attempted metabolite profiling in these accessions. This work aimed at assessing the molecular and biochemical variability in saffron since it has been reported to be highly stable in other parts of the world. Various primer combinations were used in SSAP and REMAP for PCR amplification and the primers giving the best pattern were used for further analysis. The retrotransposon based molecular marker failed to find any variation at molecular level inferring the inability of retrotransposon mobility to cause polymorphism in geographically different cultivars of Crocus sativus. However, the HPLC profiling of samples collected from 17 selected locations among the thirty samples, revealed variations in metabolite concentrations of crocin and safranal. The results obtained in this study supported the monomorphic nature of Kashmir saffron at genetic level.