India holds a rich genetic diversity of yams and the occurrence of about fifty different Dioscorea species was reported, largely in the west, east and northeastern regions. Among the Dioscorea species, greater yam (Dioscorea alata L.) is the most important species grown throughout India. The National Repository on Tuber Crops Germplasm at Central Tuber Crops Research Institute, India conserves 431 accessions of greater yam as field gene bank. Wide variability for tuber shape, flesh colour, plant architecture and other morphological, biochemical and agronomic traits were recorded among accessions in the field gene bank. In the present study, morphological and molecular characterization was carried out in greater yam accessions collected from 14 states representing the major yam growing regions in India. A total of 48 morphological traits were recorded using International Plant Genetic Resources Institute (IPGRI) descriptors. Ten microsatellite markers were screened and seven polymorphic markers were used for molecular characterization. The results showed the divergence of the genotypes between southern states adjoining Western Ghats and north eastern states that form the two hot spots of biodiversity. Several triploids with high dry matter content (>35%) and compact tuber shape were isolated. This paper depicts the wide spectrum of variation present in greater yam native to India and its use in developing hybrids with value added traits.