Surgical site infections are common following surgical procedures, despite aseptic technique and prophylactic antibiotic use. Although gut commensals are believed to limit certain infections in the intestine, an analogous role for skin commensals has not been described. To identify bacteria with the potential to protect against infection, we characterized the wound microbiome in 52 patients who underwent skin cancer surgery and healed without signs or symptoms of infection. Compared to intact, non-operated skin from the same patients, we observed several species of bacteria with significant differences in relative abundance one week after surgery.