Two new species of Schoenocaulon from Mexico, S. framei and S. oaxacense, are delimited by analyses of ITS sequence data and characterized by distinct morphology and biogeography. Schoenocaulon framei, a segregate from the polyphyletic S. comatum s.l., is described for the first time; S. oaxacense is elevated to species rank, based on S. caricifolium var. oaxacense, one of two monophyletic varieties comprising polyphyletic S. caricifolium s.l. Schoenocaulon framei is distinguished by unusual sunken stomata on the abaxial leaf surface and ligulate, weakly auriculate tepals, each with a smooth basal nectariferous zone; the basal perigonal gland of S. oaxacense is a glandular depression, and its tepals are ligulate. Both new species also are well-supported cladospecies with ITS sequence data according to the apomorphic species concept. Our results confirm the importance of molecular phylogenetic analyses in decisions relating to species circumscription, especially when such analyses are carefully correlated with morphological markers. The study also demonstrates the ease in applying the major phylogenetic species concepts and suggests that the apomorphic and diagnostic phylogenetic species concepts may result in identical specific circumscriptions.