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Summary: The Mekong River Basin in South East Asia has experienced in recent decades large inter-annual variations between large floods and severe droughts. The general perception is that climate variability has increased in the region. In this paper our aim was to examine the role of El Niño-Southern Oscillation (ENSO) on these recent climate variations. To achieve our aim, we analysed the influence of ENSO on precipitation (over period 1981–2005) and discharge (1910–2008) by using spatial GIS analyses and statistical methods, such as linear correlations, spectral analysis and stochastic regression models. We found that the Mekong’s hydrology was significantly influenced by ENSO, particularly in the decay year of ENSO events. The influence was strongest in the southern parts of the basin. The precipitation and discharge decreased (increased) during El Niño (La Niña) and the annual flood period was shorter (longer) during El Niño (La Niña). We found also decadal variations in the ENSO-discharge relationship. Our findings indicate high potential for developing prediction methods for ENSO induced hydrological anomalies. These findings may significantly improve the possibility of preparing for extreme hydrological events, either drought or exceptional floods, and thus potentially improve water resources management in the basin. [ABSTRACT FROM AUTHOR]