Species of Ceratocystis commonly infect wounds on trees. In this study, artificially induced wounds were made on the stems of Eucalyptus, Schizolobium and Terminalia trees in Ecuadorian lowland forests, in an effort to determine the presence of Ceratocystis spp. in that environment. Species belonging to the C. fimbriata sensu lato (s.l.) complex and others in the C. moniliformis s.l. complex were collected. Phylogenetic analyses for both major groups in Ceratocystis using three gene regions (ITS, β-tubulin and EF1-α) revealed three distinct clades in the C. fimbriata s.l. complex and two in the C. moniliformis s.l. complex. Isolates in the three clades representing the C. fimbriata s.l. complex represent morphologically distinct species that are described here as C. curvata sp. nov., C. ecuadoriana sp. nov. and C. diversiconidia sp. nov. Isolates in one of the two clades in the C. moniliformis species complex represented C. moniliformis sensu stricto (s.s.) and the other was of a species with a distinct morphology that is described here as C. sublaevis sp. nov.