The parentals of the interspecific cross Cucurbita maxima xC. ecuadorensis had different isozyme phenotypes for 12 enzyme systems. Characterization of the systems demonstrated that the expression and intracellular distribution of the isozymes were similar to those in other plant taxa; however, a considerable number of duplicate loci were identified, indicative of a polyploid ancestry for Cucurbita. Genetic analysis provided evidence for 20 loci segregating in F(2) and backcross populations. Five linkage groups were identified, consisting of the loci Aat-mb - - Mdh-m2; Gal-1 - - Gal-2; Aat-p2 - - Gpi-c2; Acp-1 - - Pgm-c2 - - Pgm-p; and Est-1 - - Tpi-c2. Significant deviations from Mendelian segregation ratios were observed in 14% of the data sets for individual loci. However, these instances were scattered among the loci, no single locus consistently displaying skewed ratios. Recombination frequencies between linked loci were similar to those observed in intraspecific crosses, and the ratio of heterozygous to homozygous genotypes in backcross populations was very close to one. These results suggest that small differences in chromosome structure were not the major cause of the loss of fertility observed in F(2) and backcross populations.