Several Drosophila species (Diptera: Drosophilidae) have become serious economic pests of berry and soft-skinned stone fruits around the world. Prominent examples are Drosophila suzukii (Matsumura), D. melanogaster (Meigen), D. hydei (Sturtevant), and D. immigrans (Sturtevant). Information on the biology and ecology of Drosophila is important for a better understanding of these important fruit pests and, ultimately, for fruit protection. In this study, the gut bacteriomes of these four Drosophila species were surveyed and the differences among bacterial communities were characterised. The 16S rRNA genes of gut microbes were sequenced by Illumina MiSeq technology (Illumina, San Diego, California, United States of America), followed by α-diversity and β-diversity analyses. The results show that bacteria of the family Enterobacteriaceae (Kluyvera and Providencia; phylum Proteobacteria) dominated all four Drosophila species. Specific dominant gut bacterial communities were found in each Drosophila species. The dominant families in D. melanogaster and D. suzukii were Enterobacteriaceae, Comamonadaceae, and Acetobacteraceae. In the intestine of D. hydei, Enterobacteriaceae had a proportion of 56.99%, followed by Acetobacteraceae, Spiroplasmataceae, and Bacillales Incertae Sedis XII. In D. immigrans, besides Enterobacteriaceae, Alcaligenaceae, Flavobacteriaceae, Xanthomonadaceae, Comamonadaceae, and Sphingobacteriaceae also had high relative abundance. These data expand current knowledge about the putative function related to gut microbes – for example, the metabolism of carbohydrates, amino acids, inorganic ions, lipids, and secondary metabolites. This knowledge provides a basis for further metatranscriptomic and metaproteomic investigations.