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The traditional cultivation of an endangered species, Diospyros riojae, in North-Central Mexico, and the sale of its fruit, is described for the first time. This is complemented by the first examination of genetic structure in New World Ebenaceae. Genetic comparisons are made among 27 accessions of D. riojae from across its known range of cultivation, and individuals of Diospyros conzattii, Diospyros digyna, Diospyros californica, Diospyros rosei, Diospyros rekoi and an unknown species of Diospyros from Oaxaca, Mexico. Morphological comparisons are made between D. conzattii, D. riojae, and the unknown species of Diospyros from Oaxaca. D. riojae is cultivated in two markedly different climates: arid and semi-arid localities west of the Sierra Gorda, especially near Tecozautla, Hidalgo, and humid areas of the Huasteca Region, east of the Sierra Gorda. Much lower levels of genetic diversity were detected in western populations, where populations are larger, and management intensity is the greatest. Neither the results of our genetic analysis, nor our morphological analysis of recent collections of D. riojae, D. conzattii, and an unknown species from Oaxaca, are consistent with the most recent revision of Neotropical Diospyros. Taxon-level divergence, rather than cultivar-level divergence, is suggested for D. riojae and D. conzattii.