Calyptranthes is the largest clade of Myrcia s. l., and is a group of considerable diversity in the threatened Atlantic forest biome of Brazil, as well as in the Amazon, Caribbean, and Cerrado. Here an expanded, geographically and morphologically representative sample of Calyptranthes is tested for monophyly; the majority of species are shown to emerge as a monophyletic clade embedded within Myrcia s. l. A single species, Calyptranthes multiflora, emerges in an independent clade, suggesting wider non-monophyly. Patterns of relationships within the group are detected, and these correlate more closely with geography than with morphology, and suggest that the oldest lineages of Calyptranthes are from what is now the Amazon forest, with later radiations to the Caribbean, Atlantic forest, and Cerrado biomes.