Background: The genus Olmeca comprises five species, two of which produce bacoid caryopses, while the rest produce typical caryopsis fruits. Olmeca species have a collective geographical distribution in Mexico and Honduras. Previous studies have suggested the potential monophyly of this genus based on plastid markers, but with inconclusive internal phylogenetic resolution. Questions: Will O. recta and O. reflexa form a monophyletic group? Will the remaining three Olmeca species form a second clade? Studied species: Olmeca. Study site and dates: Mexico. Methods: We collected samples from five Olmeca species and employed nuclear single nucleotide polymorphisms derived from restriction-site associated DNA sequencing data to construct our phylogenetic hypothesis using maximum likelihood and coalescent methods. We estimated divergence times using the RelTime method and performed ancestral reconstruction of geographic areas using S-DIVA analysis. Results: The SNP data supports the monophyly of the genus Olmeca and the existence of two distinct clades, Fulgor and Reflexa. Our estimate suggests that Olmeca originated approximately 7.2 million years ago. The inferred ancestral areas point to Veracruzan + Chiapas Highland provinces or the Veracruzan + Sierra Madre del Sur provinces as the likely origin of the genus. The biogeographic distribution of Olmeca can likely be explained by a combination of dispersal and vicariant events. Conclusions: The analyses recovered O. recta and O. reflexa as a monophyletic clade. Additionally, the remaining three Olmeca species formed a second clade, with O. fulgor as the sister species to O. zapotecorum, consistent with their morphological similarities.