Several accessions of Dioscorea, a tuber crop of the family Dioscoreaceae, have been conserved under field and in-vitro conditions at the Plant Genetic Resources Center, Sri Lanka. Therefore, identification of duplicates in the collection is necessary as they cause a considerable wastage of input during the conservation process and leads to confusion when using these accessions in plant variety improvement programs. In this study, 21 Dioscorea accessions belonging to Dioscorea alata, D. esculenta, D. bulbifera and D. pentaphylla were characterized by 75 morphological characters and 15 simple sequence repeat (SSR) markers. The morphological characters were distributed as; 31 leaf, 21 stem, five flower and 18 tuber characters. The dendrogram showed that there are four main clusters without duplication. Accession 107 recorded as D. pentaphylla was well separated from other accessions while four accessions (21, 36, 113 and 92) were clustered into non-related clusters with their species. The SSR analysis was conducted on 20 Dioscorea accessions (except for the accession 107) through Power Marker. Polymorphism was detected among all Dioscorea accessions with 2 to 5 alleles per marker and a genetic distance ranging from 0.1333 (among accessions 101, 102, 103 and 109) to 0.7529 (between accessions 83 and 133). The phenogram resulted in three major clusters, which is almost in agreement with the existing classification. A disagreement was observed with respect to the accession 36 recorded as D. alata and 127 recorded as D. bulbifera as both were clustering with D. esculenta. Duplicates, accession 113 and 101, were classified with D. bulbifera and accession 62, 26 were identified with D. esculenta, respectively.