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Principal component analyses of variation at 21 isozyme and 43 random amplified polymorphic DNA (RAPD) loci in eight cucumber (GY-14a, G421, H-19, WI 2757, and PIs 432860, 458845, and 183967) and seven melon [Top Mark (TM), Doublon, Green Flesh Honeydew (GFH), Juane Canari (JC), Freeman cucumber (FC), Snakemelon (SM), and PI 124111] cultigens were used to determine the use of these markers for assessing genetic variation among and within populations of each species (outgroup = Cucumis metuliferus). RAPD and isozyme marker variation was related to previous taxonomic classification and available pedigree information. Although dendrograms derived from cluster analyses using species' variation at marker loci were dissimilar, these disparities were consistent with differences in the pedigrees and/or other information (e.g., morphological) known about each accession and species. Elite U.S. processing cucumbers (G421, GY-14a, and H-19) shared distinctive biochemical affinities. Doublon was differentiated from TM, GFH, and JC. Doublon had biochemical affinities with FC, SM, and PI 124111.