Technical Abstract: In this study, we investigated the response of the microbial communities in manure-amended and unamended soil treated with either propargyl bromide (PBr) or 1,3-dichloropropene (1,3-D) at a rate of 10, 100, and 500 mg kg-1. After treatment of the soils, the metabolic activity was assessed by monitoring dehydrogenase activity (DHA) and substrate-induced respiration (SIR). At PBr and 1,3-D concentrations of 10 and 100 mg kg-1, the DHA and SIR in amended soil was found to be higher than in corresponding unamended soil. Community level changes were monitored over a 12-week period using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA fragments. Dominant bands all but disappeared upon the 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 in each of the fumigated samples. In unamended and amended soil, the community diversity decreased with increasing concentrations of PBr and 1,3-D; however, this effect was less dramatic in the manure amended soils. At 1, 4, 8, and 12 weeks, major bands were excised from the gels and the DNA was cloned for sequence analysis.