Protothecosis is a disease caused by unicellular, achlorophilic, saprophyte, and opportunistic algae of the genus Prototheca, affecting mainly animals with immunodeficiencies. In canines with the intestinal form, it causes bloody diarrhea, which can progress to a systemic disease. At the same time, skin lesions are common in felines. In Costa Rica, P. zopfii is the species identified with the highest frequency, and P. wickerhamii was identified once. Prototheca spp. can be diagnosed using different techniques, such as cytology, histopathology, endoscopy, culture, polymerase chain reaction, biochemical method, and others. Currently, the recommended treatment is the use of amphotericin B and itraconazole, which have been reported to be effective in felines; however, there is no effective treatment in canines with systemic disease. Surgery is recommended in cases of cutaneous lesions.