One of the basic strategies for floods control, is identify and spatial prioritization of flood prone areas within a watersheds. However, several methods have been introduced to identify flood generation areas, but in recent years a new method called "Successive Single Sub-watershed Elimination (SSSE)", is used to identify sub basins that contributed to flood generation in a catchment. In this method, the flood potential areas are determined by hydrograph analysis in watershed outlet; while the maximum flood may not occur in watershed outlet. Thus, it is necessary to investigate the whole tributaries and sub- watersheds in order to determine the location of maximum flood formation. In this article employ the above approach to determine flood prone areas in Shamsabad basin using stream-flow routing technique. The Shamsabad basin with an area of 1680 km ² and an elevation range of 1,200 to 2,500 meters was divided into 28 sub-basins. Sub-basin physical characteristics were measured in geographical information system (GIS). Design storm return period for 2, 5, 20, 50 and 100 years in 2, 5 and 12 hour duration were calculated using meteorological data. Then hydrologic HMS model was run. The results showed that the highest flood rate has occurred in the central basin at junction-5. The only half of the upper parts of watershed contributed in this junction flood. It was concluded that identification and prioritization of the risk of flood prone areas should be based on the location of maximum flood within the catchment not rely on outlet hydrograph analysis. Prioritization of flood prone areas showed that, the B sub-watershed has the most contribution in J-5 flood formation and after that are C, A, G1 and H1 sub-watersheds.