Soil erosion is a natural process and has been occurring in most areas in the watershed. However, accelerated soil erosion rates have been causing numerous environmental impacts in recent years. To reduce soil erosion and sediment inflow into the water bodies, site-specific soil erosion best management practices(BMPs) need to be established and implemented. The most commonly used soil erosion model is the Universal Soil Loss Equation(USLE), which have been used in many countries over 30 years. The Sediment Assessment Tool for Effective Erosion Control(SATEEC) ArcView GIS system has been developed and enhanced to estimate the soil erosion and sediment yield trom the watershed using the USLE input data. In the last decade, the Soil and Water Assessment Tool(SWAT) model also has been widely used to estimate soil erosion and sediment yield at a watershed scale. The SATEEC system estimates the LS factor using the equation suggested by Moore and Burch, while the SWAT model estimates the LS factor based on the relationship between sub watershed average slope and slope length. Thus the SATEEC and SWAT estimated soil erosion values were compared in this study. The differences in LS factor estimation methods in the SATEEC and SWAT caused significant difference in estimated soil erosion. In this study, the difference was -51.9%(default threshold)${sim}-54.5%$(min. threshold) between SATEEC and non-patched SWAT, and -7.8%(default threshold)${sim}+3.8%$(min. threshold) between SATEEC and patched SWAT estimated soil erosion.