With approximately 1080 species, Sonerileae is the second‐largest tribe in the Melastomataceae. Approximately 40% of the Sonerileae species belong to fleshy‐fruited genera (Catanthera, Heteroblemma, Kendrickia, Medinilla, Pachycentria, Plethiandra). Relatively few species, especially of the fleshy‐fruited taxa, have been sampled for phylogenetic study. Consequently, there is huge uncertainty resulting in many unanswered questions about their evolutionary history, including the monophyly of the largest genus, Medinilla. In this study, the phylogeny of the fleshy‐fruited Sonerileae was reconstructed using 385 nuclear and 81 plastid protein‐coding loci recovered from newly generated target capture and off‐target reads data, and previous studies. Our study revealed that the fleshy fruited Sonerileae belong to three lineages. Kendrickia is sister to an Afrotropical endemic clade. Heteroblemma and Catanthera belong to a second clade and are most closely related to some Phyllagathis and Driessenia species. Medinilla forms a third clade that also includes Pachycentria and Plethiandra. Within Medinilla, 15 clades are identified and characterized. To make Medinilla monophyletic, the genus is redefined to include Pachycentria and Plethiandra. Major lineages identified within Medinilla lay the groundwork for an infrageneric classification system. Areas of the phylogenetic tree with high conflict or weak sampling are identified to aid further studies in the tribe.