Cucurbita pepo is an economically important crop, which consists of cultivated C. pepo ssp. pepo, and two wild taxa (C. pepo ssp. fraterna and C. pepo ssp. ovifera). We aimed at understanding the domestication and the diversity of C. pepo in Mexico. We used two chloroplast regions and nine nuclear microsatellite loci to assess levels of genetic variation and structure for C. pepo ssp. pepo’s landraces sampled in 13 locations in Mexico, five improved varieties, one C. pepo ssp. fraterna population and ornamental C. pepo ssp. ovifera. We tested four hypotheses regarding the origin of C. pepo ssp. pepo’s ancestor through Approximate Bayesian Computation: C. pepo ssp. ovifera as the ancestor; C. pepo ssp. fraterna as the ancestor; an unknown extinct lineage as the ancestor; and C. pepo ssp. pepo as hybrid from C. pepo ssp. ovifera and C. pepo ssp. fraterna ancestors. C. pepo ssp. pepo showed high genetic variation and low genetic differentiation. C. pepo ssp. fraterna and C. pepo ssp. pepo shared two chloroplast haplotypes. The three subspecies were well-differentiated for microsatellite loci. C. pepo ssp. fraterna was probably C. pepo ssp. pepo’s wild ancestor, but subsequent hybridization between taxa complicate defining C. pepo ssp. pepo’s ancestor.