A review of live, herbarium, and bibliographic material of Chelyorchis revealed considerable floral variation that appears to be geographically correlated. We assessed whether the genus included one or more taxonomic entities using a morphometric analysis that involved the study of principal component analysis across several floral characters in 70 specimens, representing both geographical range and morphological variation. To further establish the phylogenetic relationships of Chelyorchis within the Cuitlauzina-clade, and to analyze the evolution of relevant characters, we performed a combined analysis using nrITS, morphological, and gap-coding data, which included only 13 species. Both of our phylogenetic analyses strongly support the genus Chelyorchis as a monophyletic entity that is sister to a clade comprised of the genera Ticoglossum and Rossioglossum. The morphometric evidence strongly suggests that two taxa at the level of species should be recognized, differing primarily in the shape and proportions of the labellum but also in their geographical distribution. A new species, Chelyorchis pardoi, is described and illustrated to accommodate the South American morph. Full description of the new species and iconography of both taxa are provided, and diagnostic features are discussed. The conservation status of the new taxon is assessed against IUCN criteria.