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To improve our understanding of the Atlantic Forest responses to climate changes in space and time, it is essential to explore how the Brazilian Atlantic rain forest is structured as observed in modern pollen assemblages and which climate parameters determine these patterns. In this context, we compiled 196 modern pollen samples including 125 from the Atlantic Forest biome and assigned each sample to one or more eco-physiognomies. We identified seven eco-physiognomies of which four clusters of one or two eco-physiognomies were clearly distinguished, namely (1) Araucaria forest with high elevation grassland, (2) lowland rain forest, (3) semi-deciduous with riverine forests and (4) northeastern Atlantic rain forest. Climatically distinct, these clusters reflect a general temperature increase and precipitation increase from the first to the fourth cluster. Furthermore, comparison of the modern pollen dataset with the Colonia pollen record from southeastern Brazil revealed that vegetation attributed to Araucaria forest with high elevation grassland showed an important variability with several shifts towards the lowland rain forest. As illustrated by comparison with the long fossil pollen record of Colonia, developing such a modern training set is crucial for the understanding of responses of Atlantic Forest to environmental changes. However, additional samples are still necessary to improve characterization of different eco-physiognomies at a local scale following a defined floristic and climatic gradient. This sampling effort is becoming increasing urgent as a result of strong biodiversity loss and habitat destruction in this region.