This study was conducted to investigate microbial organisms that can be used for preventing clogging in drip irrigation systems caused by biological factors. A total of 25 fungi isolate and 121 bacterial strains were isolated from water samples collected from drip irrigation systems in tomato greenhouses in the eastern Anatolia region of Turkey in the spring season of 2001. Biological clogging of emitters in a model drip irrigation system was experimentally caused by application of the microorganisms (fungi and bacteria) isolated in the study. Three antagonistic bacterial strains in the genus Bacillus spp (ERZ, OSU-142) and Burkholdria spp (OSU-7) were used for treatment of biological clogging of the emitters. The results showed that the antagonistic bacterial strains tested have the potential to be used as anti-clogging agents for treatment of emitters in drip irrigation system. This is the first study that demonstrated that antagonistic microorganisms can be utilized for treatment of clogging in drip irrigation systems.