A better understanding of the structure and extent of genetic variability in a breeding population of a crop is essential for translating genetic diversity to genetic gain. We assessed the nature and pattern of genetic variability and differentiation in a panel of 100 winged-yam (Dioscorea alata) accessions using 24 phenotypic traits and 6,918 single nucleotide polymorphism (SNP) markers. Multivariate analysis for phenotypic variability indicated that all phenotypic traits assessed were useful in discriminating the yam clones and cultivars. Cluster analysis based on phenotypic data distinguished two significant groups, while a corresponding analysis with SNP markers indicated three genetic groups. However, joint analysis for the phenotypic and genotypic data provided three clusters that could be useful for the identification of heterotic groups in the D. alata breeding program. Our analysis for phenotypic and molecular level diversity provided valuable information about overall diversity and variation in economically important traits useful for establishing crossing panels with contrasting traits of interest. The selection and hybridization of parental lines from the different heterotic groups identified would facilitate maximizing diversity and exploiting population heterosis in the D. alata breeding program.