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Savanna patches are features of the Amazonian landscape that have been long under intense debate, but there are still questions about the main factors that have determined their establishment and evolution within the rainforest matrix. In particular, their geological substrates were poorly documented. The aim of this work is to reconstruct the tectono-sedimentary history of four savanna patches in the middle Madeira River, southwest Amazonia, and discuss its potential control over the development of the savanna communities. The approach consisted in the integration of geomorphological, sedimentological, chronological and floristic data. The results revealed that the savanna substrates are sandy deposits aged between 118.9 and 35.6 ky, overlain by late Pleistocene to Holocene muddier successions < 25,700 cal yr BP. Most of the geologically stable and topographically higher terrains of the geomorphological unit T1 is dominated by forests. These intermingle with open habitats formed by renewed sedimentation that were colonized by tree and shrub species of the Amazonian biome. By contrast, the ground of unit T2 subsided to a level that allowed the meandering of the main river. This process resulted in the replacement of the rainforest by open habitats dominated by savannas with lower richness and diversity than in the T1 unit, which were dominated by species with wide distribution in the cerrado biome of Central Brasil. The cerrado species might have expanded into this region during Pleistocene drier climatic episodes, but environmental filters shaped by geological processes determined the floristic contrasts between units T1 and T2. The lack of competition with Amazonian species probably constituted an important factor for the preferential colonization of arboreal and shrubby species from neighboring cerrados on meandering scroll bars, marginal levees and crevasse splays of unit T2.