Morphological data have produced conflicting results when analyzing evolutionary relationships within Gesneriaceae due to convergence of morphological characters. Columnea, the largest Neotropical genus in Gesneriaceae subfamily Gesnerioideae, has had a convoluted taxonomic history due to this convergence. Previously, the 200 species of Columnea were placed in 14 genera, with up to nine sections in the genus; most recently classifying the species in a single genus with five sections. Phylogenetic analyses presented here included 129 accessions representing 90 species for five chloroplast gene regions (trnQ-rps16 spacer, rpl32-trnL_UAG spacer, rps16 intron, trnS-G spacer, and trnH-psbA spacer) and nuclear ribosomal ITS to build a well-supported topology that can test the previously proposed subgeneric classifications. Our goal was to test the monophyly of section Stygnanthe, one of the five sections that encompasses 18 species based on floral morphology. Fifteen species of Stygnanthe and four species that had not been classified in Stygnanthe but shared similar floral morphologies were included in the molecular phylogenetic analyses. Analyses indicate that the 19 species with a similar floral morphology belong in four separate clades including a newly proposed section, Columnea section Angustiflorae. Of the remaining three species with similar morphologies that were not sampled, only one is proposed to be a member of section Angustiflorae, none are members of clade Stygnanthe, but are likely to belong in other clades.