The molecular fingerprinting technique (PCR-DGGE) of microbial populations was successfully adopted for soilless culture systems. Relatively low concentrations of micro-organisms in the nutrient solutions could be assessed. PCR-DGGE was applied in several experiments to compare the composition and diversity of the bacterial populations in different treatments, as well as at different locations and ages of the crop. Although numbers of culturable aerobic bacteria were similar in different rockwool treatments, the PCR-DGGE patterns showed that the bacterial composition and diversity differed. The bacterial composition in treatments which were suppressive to Pythium aphanidermatum (i.e. previously used rockwool and used rockwool that was recolonised after autoclaving) differed from that in autoclaved used rockwool with a high disease incidence. Additionally, a shift in the bacterial populations during plant growth was seen. Samples of the nutrient solution from different locations in a closed soilless culture system, i.e. drain, effluent, and solution in the rockwool slabs, showed different banding patterns. The results summarised in this paper showed that PCR-DGGE is a powerful tool to study the microflora under different conditions.