Paecilomyces variotii (P. variotii) is an extremely rare cause of continuous ambulatory peritoneal dialysis (CAPD) peritonitis. When diagnosed, it usually portends poor prognosis. Patient's survival depends on early laboratory diagnosis and proper treatment. We herein report a P. variotii peritonitis in a patient on CAPD which is a quite rare clinical entity. Laboratory diagnosis was confirmed via both morphological analysis and DNA sequencing. Antifungal susceptibility tests were performed and interpreted according to the Clinical Laboratory Standards Institute M38-A2 guidelines. After laboratory diagnosis, the patient was treated succesfully with liposomal amphotericin B and itraconazole combination and the peritoneal catheter was removed. This case is worthy of reporting since P. variotii is an uncommon cause of peritonitis and leads to dilemmas in both laboratory diagnosis and treatment strategies.