Prototheca species have been reported to cause infections in human. Typically, clinical symptoms of protothecosis include cutaneous infection, olecranon bursitis, tenosynovitis and disseminated systemic disease. We report a case of septic arthritis in which Prototheca zopfii was isolated from blood. Joint aspirate was also sent for cultures but did not yield any growth. No other organisms were isolated from this patient during his admission. The blood isolate was identified to species level via Polymerase Chain Reaction (PCR) method. The patient improved with administration of intravenous itraconazole.