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A modeling exercise is performed to test and compare the ability of SWAT and APEX watershed models for implementation in watershed management at Micro-watershed level. Data obtained from Regional Research Laboratory Bhopal in Madhya Pradesh, India for Dudhi watershed were processed and converted to SWAT required format using GIS technologies. Watershed delineation application of AVSWAT were used to demarcate subbasins and to generate the topographic variables as required by APEX to build the subarea file, indicating routing mechanism as used for the study area. The SWAT and APEX models were run independently with the set up of input data for individual model and simulated discharge by both the models were compared with observed discharge data for the period 20/7/2000 to 30/9/2000 (for the period which the data on observed discharge were available). Results indicate that both SWAT and APEX models were able to replicate the daily variation in observed flow for the study period. SWAT underestimated the observed flow during peak flow period and over estimated the observed flow during low flow period. In contrast APEX overestimated the observed flow during peak flow period and underestimated the observed flow during low flow periods. R2 values obtained from scatter diagram plotted between observed and simulated flow for both the models indicate that APEX model is able to simulate the flow with slightly greater degree of confidence as compared to that with SWAT. Therefore while both model can be applied for watershed management in the study area but ability of the APEX model to simulate water balance at higher spatial resolution i.e. at plot level makes it more appropriate tool for watershed management at field or micro watershed level.