A long term experiment of rice-wheat rotation system sprayed in wheat with clodinafop continuously and as a component of herbicide rotations has been conducted on a permanent plot at Regional Research Station, Karnal since 1999. During the rabi season of 2005-06, wheat rhizosphere soil samples of above experiment were analyzed for total bacterial, free living diazotrophs and nitrifying bacterial populations in green manured plots (GM) and in plots without green manuring (WGM). Total bacterial and free living diazotroph populations were more in GM plots than in WGM plots. At early stages after the application of clodinafop, bacterial population was significantly less in plots sprayed with clodinafop as a component of herbicide rotations than in plots sprayed with clodinafop continuously and weedy control. At 30 days after the clodinafop treatment (DAT), free living diazotroph count was less in clodinafop treated GM plots than controls (weedy and weed free). The nitrifying population was inhibited at early stages after the application of clodinafop under GM conditions.