The Neotropical clade of Lecythidaceae—Lecythidoideae—comprises 10 genera and more than 230 woody species that are usually rainforest trees. Lecythidoideae range from Mexico to southeast Brazil but are most diverse and abundant in the central Amazon and Guiana Shield regions. Previous studies found weak support for monophyly in the two species rich Amazon-centered genera, Eschweilera and Lecythis, and ambiguous relationships within the Bertholletia clade (Eschweilera, Lecythis, Bertholletia and Corythophora). We performed a phylogenomic analysis of Lecythidoideae with focus on the Bertholletia clade, using target capture sequencing of 343 nuclear loci and 10 informative plastome regions. Our sampling included 206 individuals from 130 described Neotropical species and ca. 10 undescribed taxa. Our limited sampling outside the Bertholletia clade confirmed the monophyly of Grias, Gustavia, Couroupita, Allantoma, Cariniana, and Couratari. Within the Bertholletia clade, however, our work shows that Lecythis and Eschweilera, as currently circumscribed, are polyphyletic. To align Lecythidaceae taxonomy with phylogeny, we propose six genus name changes within the former Lecythis and Eschweilera. Our new circumscription maintains the core Lecythis (Ollaria clade) and Eschweilera (Parvifolia clade). For the clade comprising the Poiteau and Chartacea sections of Lecythis we reinstate Chytroma Miers. For the former Pisonis section of Lecythis we reinstate Pachylecythis Ledoux. For the former Tetrapetala section of Eschweilera we propose Imbiriba gen. nov. For the Corrugata clade (formerly of Lecythis) we propose Guaiania gen. nov. We propose to elevate the Integrifolia clade of Eschweilera as a new genus, Scottmoria gen. nov. We determined that the Manaus-area endemic, Eschweilera amazoniciformis, is an isolated sister lineage to Corythophora and Imbiriba. We recognize this species as the monotypic genus Waimiria gen. nov. Our proposal for taxonomic changes highlights distinct evolutionary histories and eliminates paraphyletic and polyphyletic genera, resulting in 60 name changes for species or subspecies.