During the beet sugar campaign 1991/1992 we have characterized thermophilic bacteria from the extraction plant of an Austrian beet sugar factory in a polyphasic approach. Sodium dodecyl sulfatepolyacrylamide gel electrophoresis (SDS-PAGE) and freeze-fracture electron microscopy revealed the presence of weakly glycosylated, oblique crystalline cell surface layers (S-layers) on all sugar factory isolates. By partial 16S rDNA sequencing and DNA-DNA hybridisation it was demonstrated that the strains belong to the species Bacillus smithii. In the course of the campaign, however, different strains of B. smithii became dominant, which was demonstrated by fingerprinting using SDS-PAGE, polar lipid analysis, random amplified polymorphic DNA (RAPD) assays, fluorophore-assisted carbohydrate electrophoresis (FACE). Possible explanations for this divergence in strain development are discussed from the technological point of view.