Molecular and morphological evidence supports a new species in the genus Antiphytum from the Sierra Madre del Sur, in the state of Guerrero, Mexico, here described as Antiphytum brevicalyx. This species is unique in the genus by possessing a calyx shorter than the corolla tube at anthesis; it is similar to A. floribundum in inflorescence arrangement, but differs from that species in lacking a basal leaf rosette and having appendages on the corolla throat. According to phylogenetic analysis of nuclear ITS and plastid ndhF-rpl32 sequences representing seven of the eight North American species of the genus besides the proposed new species, accessions of A. brevicalyx form a well-defined clade within Antiphytum, corroborating its distinctive morphology. However, the analyses do not resolve the phylogenetic position of A. brevicalyx within the genus.