We have produced a near-complete phylogeny for the neotropical fern genus Danaea (Marattiaceae). The phylogeny is based on four loci of the chloroplast DNA and shows reconstructions of the evolutionary relationships between 68 of the currently recognized 81 taxa of Danaea. A parallel paper (Keskiniva & Tuomisto 2024) draws on this phylogeny to describe 18 new species; here we discuss the phylogeny and its taxonomical implications more broadly. We propose three new synonyms: D. atlantica Christenh. & al. (= D. geniculata), D. draco Christenh. (= D. polymorpha), and D. moralesiana A. Rojas (= D. erecta). On the other hand, we consider D. jamaicensis Underw., which has been synonymized before, to be a distinct species. In addition, we propose that D. xushana is a hybrid between D. simplicifolia and D. nigrescens. We also provide an open-access online key to the 81 taxa. The key is available at https://keys.lucidcentral.org/keys/v4/neo_fern_genus_danaea/.