Abstract In this study we investigated the response of microbial communities in unamended and manure-amended soil treated with the fumigants propargyl bromide (PBr) and 1,3-dichloropropene (1,3-D). The soil fumigants were applied at a rate of 10, 100, and 500 mg kg(-1). After treatment of the soils, the metabolic activity was assessed by monitoring the dehydrogenase activity (DHA). PBr and 1,3-D initially inhibited the DHA when applied at 500 mg kg(-1); however, after 8 weeks, recovery of the DHA only occurred in amended soil. Bacterial community level changes were monitored over a 12-week period after fumigation using denaturing gradient gel electrophoresis of polymerase chain reaction-amplified 16S rDNA fragments. Band numbers were drastically reduced upon application of the fumigants, but reestablished more rapidly in the amended soil. To determine changes in the community diversity, the Shannon-Weaver index of diversity, H, was calculated for all treatments. In unamended and amended soil, the community diversity decreased with increasing fumigant concentration. In the PBr-treated soils, the diversity was higher in amended soil at all concentrations throughout the study, while in the 1,3-D treatments, the results were mixed. At 1, 4, 8, and 12 weeks after fumigation, major bands were excised from the gels and the DNA was cloned for sequence analysis. The bacterial communities in the fumigated amended soils were dominated by Streptomyces spp., other genera of actinomycetales, including Frankia, Cytophagales, Actinomadura, and Geodermatophilus, and a number of unidentified bacteria. Our results suggest that it may be feasible to reduce the impact of fumigant pesticides on soil microbial populations by stimulating microbial community structure, diversity and activity through the addition of organic amendments.