A new species of Copaifera from a diversity hotspot in the Brazilian Cerrado is described. Copaifera appendiculata M.J. Silva appears to be endemic of the northern portion of Goi??s State, Brazil, and its conservation status is classified as Critically Endangered. It is a dwarf species and can be recognized by a set of characteristics that include: foliar rachis spiny and conspicuously prolonged (the first such report for the genus), leaflets similar in size, usually glabrescent on both surfaces, with planar margins, with discreet or conspicuous translucent points, sepals indumented on both surfaces, fruits glabrous, and seeds with an orange aril. It is compared with similar dwarf species of the genus present in the Cerrado, especially with Copaifera marginata, its closest congener. Also furnished are illustrations, images, information concerning its flowering and fruiting seasons, geographical distribution, as well as preliminary conservation assessments. Examinations of the leaf anatomies of the new species, as well as that of C. marginata, revealed the numbers of layers of palisade parenchyma, the presence of a hypodermis, the numbers of vascular bundles in the petiole, rachis and midrib, as well as their contours, and aspects of the leaf margins. All of those features constitute useful characters to separate the two species. Histochemical tests demonstrated that chemical compounds (e.g., alkaloids, phenolic compounds, and lipids) present in the leaf tissues of both species have potential medicinal properties.