Recent investigations of wetlands in western Amazonia have revealed the presence of extensive peat deposits up to 7.5 m thick developing under a variety of vegetation types. We report the first attempt to establish the long-term (centennial to millennial scale) vegetation history of one of these peatland sites, Quistococha, a palm swamp close to Iquitos in northern Peru. Pollen and sedimentological analyses show that peat formation began at the core site under sedge fen or floating mat vegetation c. 2200 calendar years before present (cal yr BP). A seasonally flooded woodland developed c. 1880 cal yr BP. The permanently waterlogged palm swamp which persists today began to form c. 1000 cal yr BP, with the present vegetation community established by c. 400 years ago. The vegetation at this site has undergone continuous change throughout the period of peat formation, with several abrupt transitions, and reversals and repetitions in the apparent trajectory of change. The pollen data, combined with sedimentary evidence, suggest that the dominant control on ecosystem functioning and development is the flooding regime. There appears to have been a decrease in fluvial influence over time. There is no clear evidence of direct climatic or anthropogenic influence although we cannot rule out the possibility of climatically driven hydrological changes. Our results caution against adopting a simple model of peatland vegetation succession in this region.