Genetic diversity and resulting heterotic groupings in Guinea yams (Dioscorea rotundata and D. cayenensis) and their wild relative D. praehensilis were assessed using Amplified Fragment Length Polymorphism (AFLP) genetic markers. Amplified Fragment Length Polymorphism generated DNA fingerprinting patterns of 19 varietal groups of cultivated yams and 1 wild species, D. praehensilis. Two primer combinations generated a total of 87 polymorphic loci across the 20 varietal groups analysed. Five major groups were recognized in the germplasm based on the neighbour-joining method of cluster analysis and the Statistical Analysis System multiple correspondence analysis procedure. Among these, four varietal groups which corresponded to D. praehensilis (cv. Grovota), D. cayenensis (cvs Yaobadou and Kpokpokpokpo), and D. mangenotiana (cv. Kappe-bolanda) were genetically distant from a core of 16 varietal groups of D. rotundata. Among these, two varietal groups (cvs Dobnawo and Koukou) from Cameroon clustered separately from the West African genotypes. The results of the present study showed that AFLP analysis is a sensitive and robust DNA fingerprinting technique for genomic analysis in yams.