Peritonitis is a serious complication associated with high morbidity and mortality in patients with peritoneal dialysis (PD). We present a case of PD-associated peritonitis caused by the unusual pathogen Rhizobium. After therapy failure and bacterial growth despite treatment with vancomycin and tobramycin, the treatment was changed to meropenem intravenously and ciprofloxacin intraperitoneally according to antimicrobial susceptibility testing. The patient subsequently recovered without having the PD-catheter removed. To conclude, patients with PD are one of many patient groups at a greater risk of infections with unusual microbial agents, and pathogens that normally do not cause disease should be considered as potential causes of pathology when antibiotic treatment failure occurs.