The spatiotemporal changes in abundance and biomass of heterotrophic bacteria, of three major bacterial phylogenetic groups, and of picocyanobacteria in the upper 20 m of a deep prealpine lake (Lake Zurich, Switzerland) were monitored during a seasonally persistent bloom of the toxigenic filamentous cyanobacterium Planktothrix rubescens. In addition, bacterial 16S ribosomal deoxyribonucleic acid (rDNA) sequences were collected at one instance from the bloom layer and from waters above and below this zone. P. rubescens comprised up to 70% of particulate organic carbon during summer stratification and autumnal mixis and thus by far exceeded the total biomass both of other phytoplankton and of prokaryotes. A strong negative correlation was found between the estimated basin-wide biomass of P. rubescens and of heterotrophic bacteria, and there was different spatial niche preference of filamentous vs. picocyanobacteria. Only members of the Cytophaga-Flavobacterium lineage of Bacteroidetes showed an increasing tendency of association with the P. rubescens population, in particular at the onset of autumnal mixing. Although the filamentous cyanobacterium was the dominant primary producer throughout the year, it did not seem to be a carbon source for heterotrophic bacteria at all. We conclude that P. rubescens represents a powerful competitor of autotrophic and heterotrophic prokaryotes, likely due to both its specific physiological (photoheterotrophic) properties and its protection against zooplankton grazing. This competitiveness might be regarded as another reason for its mass occurrence in numerous lakes of the Northern hemisphere.