Uncovering phylogenetic diversity is important, but not simple. A species complex is defined by different taxa with close evolutionary relationships harbouring limited morphological and/or genetic gaps. One such example exists within neotropical Utricularia sect. Foliosa, which is a taxonomically problematic assemblage composed of three currently recognized species: Utricularia amethystina. U. tricolor, and U. tridentata. The section type, Utricularia amethystina, contains 27 synonymized names. Morphological variation across the three species and associated synonyms suggests that previous taxonomic studies had underestimated taxonomic diversity. To examine taxonomic limits we sampled multiple accessions representing the three currently recognized species and many of the synonymized taxa classified under U. amethystina. We reconstructed a molecular phylogeny using three plastid regions (rps16, trnL-F, trnD-T) and nuclear ribosomal ITS. The three plastid markers produced similar phylogenetic topologies, and the combined plastid and nuclear phylogenies were congruent. The combined analysis provided strong support for most taxa previously identified through morphological analysis, also containing distinct groupings that likely represent both putative new species, and synonyms that are not monophyletic under the type accessions to which they had previously been relegated. The current analysis also shows a sister relationship between U. amethystina s. s. and U. tricolor, with U. tridentata found to be nested within the sister clade. Our results uncovered previously underestimated phylogenetic diversity within Utricularia sect. Foliosa, possibly driven by isolation factors such as specific phytophysiognomy across the varied habitats of the broad distribution across Central and South America.