Soil microbial diversity analyses may serve as a means to assess biological soil quality. However, large portions of soil microbial communities are inaccessible to analysis with standard culture-techniques which leave over 90 % of the microorganisms unaccounted for. Several alternative techniques allow for more detailed analyses of soil microbial communities. We applied analyses of (I) community DNA (PCR-RFLP), (II) phospholipid fatty acids (PLFA), and (III) substrate utilization (Biolog™ GN-plate), to evaluate the biological characteristics of three soils used in pesticide degradation studies. Each of these methods offers a focus on specific aspects of soil microbial diversity. We found that all three methods yielded highly reproducible fingerprints for each soil and allowed to distinguish the soils based on the structures of specific gene- and PLFA-pools as well as on substrate utilization characteristics. The methods are also characterized by factors such as laboratory performance, resolution, as well as the potential for extension and specification of the analyses. Results are compared and discussed with respect to their implications on monitoring and analyzing biological soil quality.