Identifying and determining the flood potential and prioritizing of the flood discharge in the sub-basins is very important in terms of watershed management, flood control and watershed management projects. In many watersheds, it is difficult to investigate and determine the impact of each of the factors and even upstream sub-basins on creating an outlet flood, especially in the sub-basins without hydrometric station. The purpose of this study was to investigate the effective parameters in the occurrence of flood in the sub-basins of Koshkabad watershed and compare the two methods of Factor analysis and rational method for flood priority. Koshkabad Basin is located in the central part of the Hamedan province and hydrologically is the main part of the Gharachay basin that it flows into the Qom lake. In this study, to determine the potential of flood sub-basins and their prioritization, First, extracted of climatic and physiographic features in sub-basins, then provided flood potential map in the sub-basins using factor analysis method. Also, using the Rational method for estimating run off coefficient, flood intensity in the sub-basins was determined by considering the effective factors in the runoff coefficient of the area including slope, landuse and soil condition and were prepared Potential map and prioritization of flood sub-basins. Comparison results of the two methods shows that the potential map of the factor analysis method is very identical to the map of the flood potential map in the Rationnal method. The final results of prioritization in both methods indicated that the Abaro, Yelfan, Mary anadg and Dareh Moradbik sub-basins with Severe and very heavy flood Are in the first to fourth priority and Siakamar, Qaraachy and Koshkabad sub-basins with a relatively low to low flood intensity are in priority from eighth to tenth priority.