Rinorea is the second most species-rich genus in the Violaceae and has a pantropical distribution. In this study we investigated relationships among species of Rinorea and tested the monophyly of newly revised infrageneric groupings of African and Malagasy species. Phylogenetic inference was based on maximum parsimony, maximum likelihood, and Bayesian analyses of plastid trnL/trnL—F and trnD—trnE regions. Results showed the divergent Neotropical Rinorea ‘Apiculata’ group to be a strongly supported clade which was consistently resolved outside of the Rinorea s.S. clade. The Rinorea s.S. clade was strongly supported and was comprised of Neotropical and Old World clades. The Old World clade was strongly supported and contained 11 clades that corresponded to newly revised infrageneric groupings of African and Malagasy species. An additional Old World clade was recovered which contained all Asian species sampled in the study and was resolved as sister to the Malagasy endemic Rinorea subsect. Verticillatae. Maximum parsimony analysis recovered two Neotropical clades, while maximum likelihood and Bayesian analyses recovered a weakly supported monophyletic Neotropical clade. This study represents the first estimation of the phylogeny of Rinorea with sampling across its distribution and breadth of morphological diversity. The results presented here have implications for generic limits in Rinorea, infrageneric taxonomy of the African and Malagasy species, and biogeography of Rinorea in Madagascar.