The microbial community of a pilot plant for the production of iron hydroxysulfates by biological oxidation of ferrous iron was studied using molecular techniques. The 16S rRNA gene libraries were dominated by one sequence type, which can be classified phylogenetically to the class of Betaproteobacteria. These bacteria have no close cultivated relatives and were also proved as the dominating species in other mine waters. The microbial community was observed over a period of 18 months using TRFLP to investigate the influence of different process parameters on the composition of the microbial diversity. These studies verified the dominance of the Betaproteobacteria in the pilot plant.