A desirable evolution towards sustainable agriculture requires taking into account potential harmful side effects of pesticides on the soil microflora. There are currently two main ways of monitoring these damaging consequences. In the past, size and activity descriptors of soil microbial communities were used. They have been criticised on the grounds that they are the net outcome of complex physiological and structural rearrangements of the soil microflora and lack the necessary sensitivity. Recent progress in analysis of microbial diversity at the species, metabolic, physiological, and genetic levels offers new promising alternatives. They have also some technical and methodological limitations.