Abstract: Field experiments were conducted to study the effect of pesticide applications on soil microbial populations in cotton agroecosystem. The pesticides were applied in test (research plot), treated (farmer) and control (without pesticides) fields. Soil samples were collected from sowing time, before and 2 days after each pesticide applications, at harvest and post harvest time during the crop seasons 1997-98. Soil samples were subjected to thawing before determining the microbial populations. Total bacterial counts (colony forming units; CFU) were determined by serially diluted samples into Luria broth media after 24 h while fungal counts were determined by Sabouraud media after 7 days incubation at 30°C. Endosulfan, profenophos + alphamethrin and methamidophos inhibited while monocrotophos and bifenthrin + acetamiprid enhanced the bacterial population. Fungal population was depressed with endosulfan while monocrotophos, methamidophos, endosulfan + dimethoate , fenpropathrin, bifenthrin + acetamiprid or with ethion or with a mixture of carbosulfan and chlorpyrifos and profenophos alone or with ethion or cypermethrin or alphamethrin stimulated. All the other applied pesticides did not cause any appreciable change in total bacterial and fungal populations. Samples collected after pesticide applications at harvest and post harvest time showed that the microbial population recovered to its normal levels at the end of each season.