The role of microbial load during aging of the adult fruit fly Drosophila melanogaster is incompletely understood. Here we show dramatic increases in aerobic and anaerobic bacterial load during aging, both inside the body and on the surface. Scanning electron microscopy and cell staining analyses of the surface of aged flies detected structures resembling abundant small bacteria and bacterial biofilms. Bacteria cultured from laboratory flies included aerobic species Acetobacter aceti, Acetobacter tropicalis, and Acetobacter pasteurianus and anaerobic species Lactobacillus plantarum and Lactobacillus sp. MR-2; Lactobacillus homohiochii, Lactobacillus fructivorans, and Lactobacillus brevis were identified by DNA sequencing. Reducing bacterial load and antimicrobial peptide gene expression by axenic culture or antibiotics had no effect on life span. We conclude that Drosophila can tolerate a significant bacterial load and mount a large innate immune response without a detectable trade-off with life span; furthermore, microbes do not seem to limit life span under optimized laboratory conditions.