The diversity of 148 greater yam (Dioscorea alata L.) accessions from the collections of the National Plant Genetics Resources Laboratory (NPGRL), Visayas State University (VSU), and the Institute of Crop Science - University of the Philippines Los Baños (ICROPS-UPLB) was evaluated using 54 Dioscorea-based SSR markers. Polymorphic bands were amplified in 50 out of 54 SSR markers with Polymorphic Information Content (PIC) values ranging from 0.65 to 0.89. Subsequent cluster analysis generated nine distinct clusters with a Jaccard’s distance index of 0.85, implying 85% dissimilarity among the greater yam accessions. Each formed cluster from the analysis comprised a varying number of accessions: Cluster I with three, Cluster II with 24, Cluster III with 15, Cluster IV with 31, Cluster V with two, Cluster VI with four, Cluster VII with 11, Cluster VIII with 27, and Cluster IX with 31 accessions. Based on the multiscale bootstrap with 5000 times resampling, the approximately unbiased (AU) p-value>0.95 was generated at Clusters II, IV, VIII, and IX with a 0.05 level of confidence. Consequently, high dissimilarity rates obtained from the molecular analysis of 148 greater yam accessions revealed high genetic diversity. Thus, eight greater yam accessions comprising PHL 33537, LA 068B, PHL 33550, PHL 31889, LA 110, LA147, TABACO, and LA 597 were potential parents for future breeding programs. Moreover, the information obtained could be essential in various greater yam improvement programs and genetic resource conservation measures.