Habenaria longissima, a new species from the H. nuda species complex, is described and illustrated. It is remarkable for the exceptionally long lateral segments of the petals and labellum, which are the longest among Neotropical Habenaria, both in absolute and in proportional terms. Despite the morphological similarity, Bayesian and parsimony phylogenetic analyses based on nuclear (ITS) and plastid DNA markers (matK), revealed that H. longissima is distantly related to other species of the complex, and constitutes an independent lineage. Its distribution is unusual in that it is the only species of Orchidaceae restricted to the Quadrilátero Ferrífero in the State of Minas Gerais and to Chapada Diamantina, in the central part of the Espinhaço range in the State of Bahia, with the populations 1000 km from each other. Habenaria longissima is a rare species, known only from three localities and four populations and informally proposed as Endangered due to the small area of occupancy and small number of known populations.