Usnea is a highly diverse lichen genus, currently including ca. 350 species that are widely distributed from polar to tropical regions. The exceptional plasticity of morphological traits towards environmental parameters causes difficulties in the circumscription of species, and taxonomic revisions are needed, especially in tropical regions. In this taxonomic treatment of Usnea in tropical South America (Bolivia, Brazil, Colombia, Ecuador, incl. the Galapagos Islands, Paraguay, Peru and Venezuela), we identified 51 species, representing ca. half of the total diversity of species occurring in this region. Out of these 51 species, 16 are so far endemic to South America, whereas several species have a wide distribution, sometimes across several continents. Twelve species were newly described and 15 species were newly reported for South America, indicating that the diversity of Neotropical Usnea species is particularly high and that numerous discoveries are yet to be made. In addition to taxonomic studies, the phylogeny of Usnea was investigated using the nuclear ribosomal genes ITS rDNA and nuLSU, as well as two protein-coding genes RPB1 and MCM7. The concatenated dataset revealed that Usnea is subdivided into four highly-supported clades, corresponding to the traditionally circumscribed subgenera Eumitria, Dolichousnea, Neuropogon and Usnea. However, phenotypic characters that have been used to characterize these subgenera are often homoplasious in the phylogeny and a parallel evolution of these characters is suggested. On the other hand, the majority of species described from phenotypic characters are monophyletic in our phylogeny. We conclude that the combinations of phenotypic characters are suitable discriminators for the delimitation of species. On the other hand, most of these characters have evolved several times independently during the diversification of the genus Usnea and are therefore inadequate to describe generic subdivisions.