A new species assigned to Erythroxylum sect. Rhabdophyllum O. E. Schulz is described and illustrated under the name of E. ayrtonianum Loiola & M. F. Sales. This new species resembles E. pelleterianum A. St.-Hil. in the general aspect of its leaves and the flexuous, slender branches, but differs by its distichous cataphylls distributed along the short branches and the leaves with wavy to strongly wavy margins. Erythroxylum ayrtonianum is reported from savanna formations (cerrado vegetation) in the north-central portion of Brazil, with the type locality from the state of Tocantins.