The genetic diversity of P. lunatus in the Yucatan Peninsula was assessed on the basis of its morphological and phenological characters. Our results were then discussed in relation to ethnobotanic information obtained about the intraspecific diversity recognized by farmers, their selection criteria, agronomic management, production purpose and percentage of cultivated area. Research was undertaken in one of the cultural subareas of Mesoamerica, the Lowland Maya area, where traditional agriculture has been more persistent and where high diversity of P. lunatus landraces has been recorded. Four of the 13 cultural-geographic zones established for the origin of this culture were included, 160 farmers from 12 localities were interviewed, and 149 seed samples of P. lunatus germplasm were collected and analyzed using six characters. A subset of these samples was grown under ex situ uniform growth conditions and analyzed using 28 characters. Ethnobotanical and morpho-phenological data indicated 30 putative distinct landraces, two wild, and two weedy variants, suggesting gene flow among them. Richness and diversity estimates were greatest, and evenness lowest, where there was: 1) minimal agricultural intensification, 2) wild and weedy populations, and 3) greater persistence of traditional culture. Results underscored the importance of establishing in situ conservation programs in these areas.