In Amazonian Peru, the neotropical tree Protium subserratum Engl. (Burseraceae) occurs as distinct ecotypes on low nutrient white-sand (WS), intermediate fertility brown-sand (BS), and nutrient-rich clay (CS) soils. Genetic analysis indicates that these ecotypes are undergoing incipient speciation. Possible drivers of this divergence are habitat-specific herbivore faunas and differing resource availabilities. Protium subserratum, therefore, provides an ideal opportunity to investigate how defense chemistry evolves during lineage divergence. WS and BS races of P. subserratum are host to largely nonoverlapping herbivore communities and they differ in chlorogenic acid, flavonoid, and oxidized terpene chemistry. Here, we investigate how another important class of anti-herbivore chemicals, procyanidins (PCs), varies among the ecotypes. We isolated the PCs from leaves of juvenile and adult trees from each ecotype and used spectroscopic and chemical techniques to characterize the chemical structures of their component monomers. We found that WS, BS, and CS ecotypes accumulate ca. 17 % of leaf dry weight as PCs. Within ecotypes, we found very little difference in PC type, neither by site nor by life stage.Among ecotypes, however, we observed a marked divergence in PC composition that arose at least in part from differences in their terminal and extension subunits. In addition, the average polymer length of BS and CS PCs was significantly greater than in WS ecotypes. We conclude that phenotypic differences in PCs in the WS versus BS and CS ecotypes of P. subserratum are consistent with selection by herbivores in different soil types that differ strongly in nutrient availability and may contribute to the evolution of habitat specialization.