Objectives As in most organisms, the surface of the fruit fly Drosophila melanogaster is associated with bacteria. In order to study the genetic parameters of this association, we developed a simple protocol for surface bacteria isolation and quantification. Results On wild-type flies maintained in the laboratory, we identified two persistently culturable species as Lactobacillus plantarum and Acetobacter pomorum by 16S rDNA sequencing. For quantification, we showered single flies for DNA extraction avoiding the rectum to prevent contamination from the gut. Using specific primers for quantitative PCR analyses, we determined the relative abundance of these two species in surface wash samples. Repeatedly, we found 20% more L. plantarum than A. pomorum . To tentatively study the importance of the cuticle for the interaction of the surface with these bacteria, applying Crispr/Cas9 gene editing in the initial wild-type flies, we generated flies mutant for the ebony gene needed for cuticle melanisation and determined the L. plantarum to A. pomorum ratio on these flies. We found that the relative abundance of L. plantarum increased substantially on ebony flies. We conclude that the cuticle chemistry is crucial for surface bacteria composition. This finding may inspire future studies on cuticle-microbiome interactions.