The microbial community of a biofilter for waste gas treatment of an animal rendering plant was characterized by the analyses of the phospholipid fatty acids (PLFAs) of the filter material. For these analyses five samples of one filter were taken in intervals between one and two months. The main components of the PLFA profiles were straight chain saturated, monounsaturated and cyclopropyl fatty acids. Terminally branched and 10-methyl branched fatty acids were present in minor amounts. The structure and succession of the microbial community was interpreted by the presence and quantitative changes of diagnostic fatty acids. The stability of diagnostic fatty acids in relation to varying incubation parameters was tested for a number of bacterial isolates from biofilters representing different phylogenetic branches. For two samples, the data from the PLFA-analyses were compared with data obtained by hybridization with fluorescently labeled, rRNA-targeted oligonucleotide probes specific for the alpha-, beta- and gamma-subclass of the Proteobacteria, the Actinobacteria (Firmicutes with high G+C content) and the Firmicutes with low G+C content. These data indicated a dominating number of Proteobacteria (54% and 35% of DAPI-stained cells), in which the gamma-Proteobacteria represented the main fraction. Actinobacteria were detected in minor amounts, the number of Firmicutes with low G+C content was near the detection limit of the method. About half of the cells detected with a probe specific for Bacteria did not hybridize with the probes specific for the alpha-, beta- and gamma subclass of the Proteobacteria and the two subgroups of the Firmicutes. The results of both methods, the fluorescence in situ hybridization (FISH) and the PLFA analyses corresponded well and were best suited to confirm and complement each other.