Three Neotropical orchid species, Mormolyca dodsonii, Mormolyca cruentata, and Mormolyca prunina are described on the basis of molecular and morphological characters. Phylogenetic relationships are estimated using sequence data from five plastid loci (rpoC1, matK gene and flanking trnK intron, atpB-rbcL intergenic spacer, and the 3′ portion of ycf1) plus the nuclear ribosomal internal and external transcribed spacers (ITS, ETS), and a portion of the low-copy nuclear gene phyC. Phylogenetic analyses confirm the monophyly of Mormolyca and clarify relationships within the genus: an early divergent paraphyletic grade of species diverging from the line leading to a major clade of two distinctive subclades. The three new species are contained within these subclades: M. dodsonii and M. cruentata clustering with the subclade characterize by flowers with a labellum pad of short glandular papillae; whereas M. prunina groups with the clade that includes all species with glossy labella.