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During 2009 the Amazon basin was hit by a heavy flooding with a magnitude and duration few times observed in several decades. Torrential rain in northern and eastern Amazonia during the austral summer of 20082009 swelled the Amazon River and its tributaries. By July 2009, water levels of the Rio Negro, a major Amazon tributary, reached at Manaus harbor a new record, the highest mark of the last 107 years. During the 20082009 hydrological year, the rainy season on northern and northwestern Amazonia started prematurely, and was followed by a longer-than-normal rainy season. An anomalously southward migration of the ITCZ during MayJune 2009, due to the warmer than normal surface waters in the tropical South Atlantic, was responsible for abundant rainfall in large regions of eastern Amazonia and Northeast Brazil from May to July 2009. We also compared the flood of 2009 with other major events recorded in 1989 and 1999. The hydrological consequences of this pattern were earlier than normal floods in Amazon northern tributaries, which peak discharges at their confluences with the main stem almost coincided with the peaks of southern tributaries. Since the time displacement of the contribution to the main stem of northern and southern Amazon tributaries is fundamental for damping flood waves in the main stem, the simultaneous combinations of peak discharges of tributaries resulted in an extreme flood.