Using cultivation-dependant method, we isolated 184 strains from fresh and old bee bread, pollen, larvae and adults of solitary bee Osmia cornuta. The 16S rDNA sequencing of 79 selected isolates gave the final species-specific identification of strains. Phylogenetic analysis indicated that microbiota isolated from five different sources were represented with 29 species within three different phyla, Firmicutes with 25 species, Actinobacteria with only one species and Proteobacteria with three species of Enterobacteriaceae. Bacterial biodiversity presented with Shannon–Wiener index (H′) was highest in the alimentary tract of adults and old bee bread (H′ = 2.43 and H′ = 2.53, respectively) and in the same time no dominance of any species was scored. On the contrary, results obtained for Simpson index (D) showed that in pollen samples the dominant species was Pantoea agglomerans (D = 0.42) while in fresh bee bread that was Staphylococcus sp. (D = 0.27). We assume that microbial diversity detected in the tested samples of solitary bee O. cornuta probably come from environment.