Background: Intestinal protothecosis is an uncommon and insidious mycotic disease. Only one human case and a few rare cases in dogs have been reported. To the authors’ knowledge, intestinal protothecosis has never been reported in cats. Case description: This paper describes a case of intestinal protothecosis in a nine-month-old male, Bengal cat. The cat presented because of onset of haemorrhagic diarrhoea. Investigations allowed diagnosis of intestinal protothecosis, confirmed by PCR test on faeces. Treatment with itraconazole did not improve the clinical signs. Treatment with nystatin was prescribed and caused improvement in the clinical signs and decreased number of pathogens seen on faecal cytology. PCR on faecal samples was negative two months after treatment, with complete resolution of symptoms. Conclusion: Infection with Prototheca should be part of the list of differential diagnoses for diarrhoea in cats. nystatin was effective in treating the infection in this case; this drug should be considered as a first-line treatment in cats as well as in dogs, in which protothecosis appears to have a poor prognosis. Although protothecosis is not considered a zoonotic disease, cases of algal infections in companion animals might be considered indicators of environmental risks for humans.