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Chlorothalonil, a non-systemic and broad-spectrum fungicide, is widely used to control the pathogens of agricul-tural plants. Although microbial degradation of chlorothalonil is known, we know little about the colonization and degradation capacity of these microbes in the natural and semi-natural soil environments. Therefore, we studied the colonization and detoxification potential of a chlorothalonil degrading Stenotrophomonas acidaminiphila probiotic strain BJ1 in the soil under green conditions. The results from polymerase chain reaction-denaturing gradient gel elec-trophoresis demonstrated that probiotic strain BJ1 successfully colonized the soil by competing with the native biota. Moreover, the bacterial inoculation stimulated some members of indigenous soil microbial communities. Meantime, the degradation half-life of chlorothalonil decreased from 9.0 to 4.9days in the soil environment. Moreover, the results from enzymatic activities and micronucleus test of Vicia faba root tips showed that the probiotic strain BJ1 reduced the ecotoxicity and genotoxicity of chlorothalonil in the soil. We suggest that probiotic strains like BJ1 could poten-tially alleviate the toxic effects of pesticides on soil microbes and plant roots under greenhouse conditions.