Technical Abstract: Principal component analyses of variation at isozyme and random amplified polymorphic DNA (RAPD) loci in eight cucumber and seven melon cultivars, breeding lines, and plant introductions were used to determine the utility of these markers for assessing genetic variation among and within populations of each species. 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. Empirical estimations of variances associated with each marker type in the accessions of cucumber and melon examined indicate that, per band, lower coefficients of variation can be attained in the estimation of genetic difference when using RAPDs compared to isozymes. The disparity between the marker analyses made may be related to the amount of genome coverage characteristic of a particular marker system in a species and its efficiency in sampling variation in a population.