An important step in flood control planning is identification of flood source areas (FSAs). This study presents a methodology for identifying FSAs. Unit flood response (UFR) approach has been proposed to quantify FSAs at subwatershed and/or cell scale. In this study, a distributed ModClark model linked with Muskingum flow routing was used for hydrological simulations. Furthermore, a fuzzy hybrid clustering method was adopted to identify hydrological homogenous regions (HHRs) resulting in clusters involving the most effective variables in runoff generation as selected through factor analysis (FA). The selected variables along with 50-year rainfall were entered into an artificial neural network (ANN) model optimized via genetic algorithm (GA) to predict flood index (FI) at cell scale. The case studies were two semi-arid watersheds, Tangrah in northeastern Iran and Walnut Gulch Experimental Watershed in Arizona. The results revealed that the predicted values of FI via ANN-GA were slightly different from those derived via UFR in terms of mean squared error (MSE), mean absolute error (MAE), and relative error (RE). Also, the prioritized FSAs via ANN-GA were almost similar to those of UFR. The proposed methodology may be applicable in prioritization of HHRs with respect to flood generation in ungauged semi-arid watersheds.