The impacts of the fungicides azoxystrobin, tebuconazole and chlorothalonil on microbial properties were investigated in soils with identical mineralogical composition, but possessing contrasting microbial populations and organic matter contents arising from different management histories. Degradation of all pesticides was fastest in the high OM/biomass soil, with tebuconazole the most persistent compound, and chlorothalonil the most readily degraded. Pesticide sorption distribution coefficient (K(d)) did not differ significantly between the soils. Chlorothalonil had the highest K(d) (97.3) but K(d) for azoxystrobin and tebuconazole were similar (13.9 and 12.4, respectively). None of the fungicides affected microbial biomass in either soil. However, all fungicides significantly reduced dehydrogenase activity to varying extents in the low OM/biomass soil, but not in the high OM/biomass soil. The mineralization of subsequent applications of herbicides, which represents a narrow niche soil process was generally reduced in both soils by azoxystrobin and chlorothalonil. 16S rRNA-PCR denaturing gradient gel electrophoresis (DGGE) indicated that none of the fungicides affected bacterial community structure. 18S rRNA PCR-DGGE analysis revealed that a small number of eukaryote bands were absent in certain fungicide treatments, with each band being specific to a single fungicide-soil combination. Sequencing indicated these represented protozoa and fungi. Impacts on the specific eukaryote DGGE bands showed no relationship to the extent to which pesticides impacted dehydrogenase or catabolism of herbicides.