The gut of insects may harbour one of the largest reservoirs of a yet unexplored microbial diversity. To understand how specific insects select for their own bacterial communities, the structural diversity and variability of bacteria found in the gut of different bee species was analysed. For three successive years, adults and larvae of Apis mellifera ssp. carnica (honey bee), and Bombus terrestris (bumble bee), as well as larvae of Osmia bicornis (red mason bee) were collected at a flowering oilseed rape field. Total DNA was extracted from gut material and the bacterial diversity was analysed, independent of cultivation, by genetic profiling with single-strand conformation polymorphism (SSCP) of polymerase chain reaction (PCR)-amplified partial 16S rRNA genes. The SSCP profiles were specific for all bee species and for larvae and adults. Qualitative and quantitative differences were found in the bacterial community structure of larvae and adults of A. mellifera, but differences in B. terrestris were mainly quantitative. Sequencing of the PCR products revealed a dominance of Alpha-, Beta-, and Gammaproteobacteria, Bacteroidetes, and Firmicutes in all bee species. Single-strand conformation polymorphism profiles suggested a higher abundance and diversity of lactobacilli in adults of A. mellifera than in larvae. Further phylogenetic analyses indicated common bacterial phylotypes for all three bee species, e.g. those related to Simonsiella, Serratia, and Lactobacillus. Clades related to Delftia acidovorans, Pseudomonas aeruginosa or Lactobacillus intestinalis only contained sequences from larvae. Several of the bee-specific clusters also contained identical or highly similar sequences from bacteria detected in other A. mellifera subspecies from South Africa, suggesting the existence of cosmopolitan gut bacteria in bees.