Not only classical cultivation-based methods but also the new molecular approaches may result in incomplete and selective information on the natural diversity of microbial communities. Flow sorting of microorganisms from environmental samples allows the deliberate selection of cell populations of interest from highly diverse systems for molecular analysis. Several cellular parameters that can be measured by flow cytometry are useful as sort criteria. Here, we report sorting of bacteria from activated sludge, lake water, and lake sediment according to differences in light scattering, DNA content, and/or affiliation to certain phylogenetic groups as assessed by fluorescein-labeled, rRNA-targeted oligonucleotide probes. Microscopy of the sorted cells showed that populations of originally low abundance could be strongly enriched by flow sorting (up to 280-fold), depending on the original abundance of the cells of interest and the type of sample sorted. The purity of the cells of interest could be further increased by repeated sorting, but this increase was limited by cell aggregation in the case of activated-sludge samples. It was possible to amplify almost full-length 16S ribosomal DNA (rDNA) fragments from sorted microbial cells by PCR, even after fixation with paraformaldehyde and in situ hybridization. Dot blot hybridization and sequencing demonstrated that most of the amplified rDNA originated from those cells that had been selected for by flow sorting. Comparative analysis of 16S rDNA sequences revealed previously unknown species of magnetotactic or activated-sludge bacteria.