In the present study, we describe and illustrate a remarkable new species of Syngonanthus from South America (Bolivia, Brazil and Peru). This new species is quickly distinguished from all species in the genus by trimerous and bisexual flowers, a unique set of characteristics in Syngonanthus. Complementary to this study, sequences of 33 species were downloaded from GenBank and four species had sequences newly generated for this study. Molecular phylogenetic analyses based on nuclear ribosomal ITS and the plastid regions psbA-trnH and trnL-F were performed to determine its systematic position. The results have shown S. androgynus closely related to a well-supported clade that has been treated as Syngonanthus sect. Carphocephalus. Floral traits associated with this new plant also were surveyed. Character reconstruction suggests that the bisexual flowers originated independently more than once in the genus. However, trimerous flowers appear to be an ancestral condition of the whole genus.