Squash and pumpkins (Cucurbita sp.) are important contributors of beta-carotene to the diet. Consumers of tropical pumpkin and butternut squash (both C. moschata Duchesne) prefer a deep orange mesocarp color. Color intensity is related to carotene content. Among the five domesticated Cucurbita species, C. moschata and C. argyrosperma Huber have a close relationship. In crosses between these two species, fertile F1 plants can be easily obtained when using C. argyrosperma as the female parent. This research studied the relationship between and within C. moschata and C. argyrosperma by sequencing three genes in the carotenoid biosynthesis pathway and generating gene trees. Genotypes used in the study differed in flesh color from very pale yellow to dark orange. In some cases, haplotypes were associated with a particular mesocarp color. Further study of these types of associations may improve our understanding of color development in Cucurbita. The frequency of single nucleotide polymorphisms (SNPs) in the sequenced fragments was low. There were more SNPs and more heterozygotes among C. moschata accessions than among C. argyrosperma accessions. Haplotypes of the outgroups (C. ficifolia C.D. Bouché and C. maxima Duchesne) were always distinct from C. moschata and C. argyrosperma. These later species had both distinct haplotypes and shared haplotypes. Haplotypes shared among species tended to be maintained in the same branch of the phylogenetic tree, suggesting either gene flow between the species or a common ancestral gene. Both explanations suggest a close genetic and evolutionary relationship between C. moschata and C. argyrosperma.