A 3-year-old girl from the Northern Territory developed suppurative keratitis after swimming in pools. A mycelial organism suspected to be Pythium insidiosum was cultured. Treatment with polyhexamethylene biguanide and voriconazole for 5 days was unsuccessful, and a corneal graft was performed. The infection was cleared and when last seen 14 months after surgery the patient had a stable graft and useful vision. The identification of the organism was confirmed by rRNA gene sequencing. P. insidiosum is an oomycete, an organism more closely related to kelp than to fungi. Masses of hyphae were seen in sections and, for the first time, the ultrastructure of P. insidiosum in human tissue is described. The staining characteristics of cultured hyphae were assessed; lactofuchsin and acridine orange were found to be the most useful methods. Although the diagnosis of P. insidiosum keratitis is not difficult, and the organism is susceptible in vitro to a number of antimicrobial agents, early corneal transplantation remains the treatment of choice.