A new species, Hymenaea jeaniana, is described and illustrated. The species is known from one of the best-sampled reserves of Amazon Rainforest, the Reserva Adolpho Ducke, in Manaus, and from protected areas of the municipality of Presidente Figueiredo, in Amazonas, Brazil. Previously, the species has been mistakenly assigned to the circumscription of the morphologically similar H. parvifolia, but differs in certain leaflet, inflorescence, and flower characteristics. The new species has a restricted distribution and is assessed as Endangered following IUCN Red List criteria. Based on herbarium collections and field studies, we present a full species description, an illustration, conservation status, and taxonomic comments. An identification key to the Hymenaea species of Brazil is also provided. There are six species of Hymenaea in the Amazon Basin, including the species described herein.