Protium section Papilloprotium and Protium alvarezianum are described and a key to the four species of the section provided. The section is distinguished principally by its papillate abaxial leaflet surface, and the petals saccate at base and villous adaxially. The rather widespread edaphic generalist P. ferrugineum shares a common ancestor with two small clades, one containing two white-sand specialists (P. reticulatum and P. alvarezianum) that appear to have diverged from a common ancestor allopatrically via fragmentation of white-sand habitats, and the other exhibiting degrees of edaphic specialization among variants of P. subserratum. This scenario highlights the role of edaphic heterogeneity as a driver in the diversification of the Amazon flora.