The taxonomically poorly known, neotropical genus Clusia (Clusiaceae) comprises over 300 species of trees, shrubs and hemiepiphytes. The flowers are morphologically highly diverse and offer either nectar, pollen or resin as a reward for pollinators. Resin production in flowers is a poorly studied phenomenon, known from only five angiosperm genera. Variation in sequences of the nuclear ribosomal ITS region was analysed cladistically in order to trace the evolution of floral resin production in Clusia, and as a first step towards a phylogenetically based reclassification of the genus. The most parsimonious trees show that the genera Havetia, Havetiopsis, Oedematopus and Quapoya are nested inside Clusia. Traditionally, Clusia has been divided into sections based on androecial variation, and most of these groups are supported as monophyletic based on the ITS data. Sections Retinostemon, Havetia and Cochlanthera together form one of very few well-supported suprasectional groups. Character optimisation experiments suggest that resiniferous flowers have evolved at least three times independently in Clusia, but a character-evolution model with a single origin for floral resin is only slightly less parsimonious. Clades of resiniferous species are morphologically the most diverse, and it is concluded that resin production has been a key innovation triggering floral morphological diversification. Secondary losses of resin and switches to apomixis seem to be correlated with colonisation of habitats and areas where resin-collecting bees are less frequent.