We describe patterns of tree community change along a 700-km transect through terra firme forests of western Amazonia, running from the base of the Andes in Ecuador to the Peru-Brazil border. Our primary question is whether floristic variation at large scales arises from many gradual changes or a few abrupt ones. Data from 54 1-ha tree plots along the transect support the latter model, showing two sharp discontinuities in community structure at the genus level. One is located near the Ecuador-Peru border, where the suite of species that dominates large areas of Ecuadorean forest declines abruptly in importance to the east. This discontinuity is underlain by a subterranean paleoarch and congruent with a change in soil texture. A second discontinuity is associated with the shift from clay to white sand soils near Iquitos. We hypothesize that the first discontinuity is part of an edaphic boundary that runs along the Andean piedmont and causes a transition from tree communities preferring richer, younger soils near the base of the Andes to those preferring poorer, older soils farther east. Because the floristic changes observed at this discontinuity are conserved for large distances to the east and west of it, the discontinuity is potentially key for understanding floristic variation in western Amazonia. The significant floristic turnover at the Ecuador-Peru border suggests that the only large protected area in the region - Ecuador's Yasuní National Park - is not adequate protection for the very diverse tree communities that cover vast areas of northern Peru.