Water vapor measurements from Aura Microwave Limb Sounder (MLS, above 300 hPa) and Aqua Atmospheric Infrared Sounder (AIRS, below 300 hPa) are analyzed to study the variations of moisture during the 2006–2007 and 2009–2010 El Niños. The 2006–2007 El Niño is an East Pacific (EP) El Niño, while the 2009–2010 El Niño is a Central Pacific (CP) El Niño or El Niño Modoki. Results show that these two types of El Niño events produce different patterns of water vapor anomalies over the tropical ocean, approximately resembling the cloud anomalies shown in Su and Jiang (2013). Regression of water vapor anomalies onto the Niño-3.4 SST for the A-Train period shows a clear “upper tropospheric amplification” of the fractional water vapor change, i.e., the ratio of the change in specific humidity to the layer-averaged specific humidity. Furthermore, tropical water vapor anomalies in different circulation regimes are examined. It is shown that the variations of water vapor during the 2006–2007 El Niño are mainly controlled by the thermodynamic component, whereas both dynamic and thermodynamic components control the water vapor anomalies during the 2009–2010 El Niño. GFDL AM2.1 model simulations of water vapor and cloud anomalies for the two El Niños are compared with the satellite observations. In general, the model approximately reproduces the water vapor anomalies on both zonal and meridional planes but it produces too strong a cloud response in the mid- and lower troposphere. The model fails to capture the dynamic component of water vapor anomalies, particularly over the Indian Ocean.