Abstract Uni-algal, non-axenic cultures of six marine diatoms were screened by polymerase chain reaction-denaturing gradient gel electrophoresis for the diversity of the accompanying bacterial communities ('satellite' bacteria) in order to test the hypothesis that algal cells constitute niches for specific bacterial species. The complexity of the satellite assemblages, as judged from the number of detected phylotypes, was low when compared to the complexity of bacterial assemblages in nature. Generally, the six algal cultures were accompanied by distinct satellite assemblages, as the majority of the phylotypes detected in the six cultures were unique, and only some phylotypes were common to more than one culture. Analysis of replicate incubations and repeated passage of cultures in most cases showed only minor variations in satellite assemblage genetic fingerprints, suggesting that the bacterial-algal associations were stable. An experimental approach to find evidence for specific bacterial-algal interactions by challenging algal cultures with heterologous satellite assemblages was unsuccessful as it was not possible to avoid carryover of algae. Satellite populations were identified by sequencing of denaturing gradient gel electrophoresis bands. Most of the populations represented typical marine phylotypes, such as members of the alpha-Proteobacteria (related to the genera Ruegeria, Sulfitobacter, Roseobacter and Erythrobacter), or members of different genera of the Cytophaga-Flavobacterium-Bacteroides (CFB) phylum. Surprisingly, beta-Proteobacteria were also found in two of the cultures. A common point for all cultures was the presence of at least one representative of the alpha-Proteobacteria and of the CFB phylum, both of which have been reported as important representatives of the marine picoplankton. Their ubiquity in the sea and in the phytoplankton cultures analysed points to a specific role of these bacteria in the marine food web. The results indicate that algal diversity might be an important factor in explaining the enormous bacterial diversity in marine assemblages, and vice versa. Specific substances in the photosynthetic extracellular release and in the organic carbon produced by different phytoplankton species may require a variety of bacterial populations for the processing of this algal-derived organic matter.