Calibrated antibody probes for homoacetogenic, syntrophic acetogenic, and sulfate‐reducing Bacteria were generated and used, along with probes for methanogenic Archaea, to elucidate the bacterial biofilm population of three fluidized bed bioreactors fed with different substrates. The new probes were for Clostridium formicoaceticum, Syntrophomonas wolfei subsp. wolfei, Syntrophospora bryantii, Syntrophococcus sucromutans strain S195, and Desulfobulbus propionicus strain 1pr3. Microscopic and electron microscopic analyses showed a complex microbial flora in the three bioreactors. This was confirmed by the antigenic fingerprinting method which showed a diversity of methanogens and syntrophs. The subpopulations that could be identified were only moderately or weakly related to reference immunotypes, and were quantitatively small. Thus, these and the major populations from the quantitative and functional standpoints, belong to as yet uncharacterized immunotypes, and possibly include new strains and species.