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AQUA AMSR-E L3 soil moisture data of 5 years (2002-06) were analyzed over Gujarat, India for flood analysis. We have used a threshold value (Gujarat 40% and Rajasthan desert 20%) for soil moisture to estimate flood affected area. Time series daily soil moisture data during flood period in Gujarat shows that soil moisture above threshold has been observed during 2004-06. The estimated flood area in Gujarat was 8418, 22618, 6313 sq. km in 2004, 05 and 06 respectively. Recent 2006 flood in Barimer, Rajasthan shows 7366 sq. km flood affected area with 20% as threshold soil moisture. The flood-area correlates well with rainfall data and surface soil moisture distribution. As the resolution of AMSR-E (60 km) is very poor, the area estimation is not so accurate. But the soil moisture trend clearly shows variation in flood affected area with days. The results from this method are to be compared with methods available using other data sets or techniques. Fixing a threshold value for soil moisture of a particular test site is also very important in the estimation of flood affected area.