Monophyly of the neotropical plant genus Alloplectus (Gesneriaceae) was tested using maximum parsimony and maximum likelihood phylogenetic analyses of molecular sequence data from the nuclear ribosomal (nrDNA) internal transcribed spacer region (ITS). As currently circumscribed, Alloplectus is polyphyletic and includes taxa in three different clades. The clade that contains the type species is described as Alloplectus sensu stricto and is characterized by the presence of resupinate flowers. The Alloplectus s.s. clade is weakly supported as the sister-group to Columnea. A separate clade of non-resupinate “Alloplectus” species nests within a paraphyletic Drymonia. A third taxon, Alloplectus cristatus, endemic to the Lesser Antilles and northwestern South America, is also resupinate and unresolved in a basal polytomy, removed from the other species of Alloplectus. The fourth taxon, Alloplectus peruvianus, which was originally described as Columnea peruviana, is strongly supported as nesting within Columnea. Resupination of flowers is an important feature that has not been previously reported and should be recognized as a morphological synapomorphy for Alloplectus s.s. Within the tribe Episcieae, flower resupination is a convergent feature that is independently derived in the Alloplectus s.s. clade, Alloplectus cristatus, and a clade comprising some Nematanthus species.