A new study of the phylogeny of Cereusinvestigates generic monophyly and previous subgeneric classification. A coalescent approach was used to assess phylogenetic relationships among Cereusspecies based on nuclear orthologous genes captured by the Cactaceae591 probe set. The analysis included two unusual new taxa from eastern and northern Brazil to ascertain their position within the genus. Amongst the additional taxa, one was found to be early derived to the Atlantic Forest and coastal Cereusspecies and is described as C. ingens. Its imposing habit, considerably broader flower, yellow fruits and large seeds differentiate it from other Cereusspecies, and its inland agresteforest habitat in Minas Gerais and Bahia leads it to be categorized as Endangered, as little remains of this vegetation type. A second new species, C. gerardi, is described from the state of Tocantins (northern Brazil). Vegetatively this taxon is remarkable for resembling members of Pilosocereus, but has typical Cereusflowers, matching those of the type of the genus, C. hexagonus. The definition and relationships of the genus within the tribe Cereeae were made more evident, partly recovering three of the four pre‐existing subgenera.