Clusia sect. Anandrogyne is the most species-rich section in the genus and it includes approximately 70 species. Taxonomic boundaries within the group have been difficult to establish due to high degree of homoplasy in morphological characters. In order to make informed taxonomic decisions, an evaluation of both morphological (fruit morphology) and molecular (nrDNA ITS) data was made among species included in Clusia sect. Anandrogyne. It was found that Clusia multiflora subsp. scariosepala has strikingly distinctive fruit morphology and, furthermore, it is phylogenetically more closely related to other species of Clusia than to Clusia multiflora. Therefore, raising this taxon to the rank of species is proposed herein. Conservation status assessment for the species is also provided.