In this study, a survey was conducted in order to determine the presence and pathogenic potential of free-living amoebae of Acanthamoeba genus in a population of Barbary Ground squirrels in Fuerteventura Island (Canary Islands, Spain) and Morocco. Identification of Acanthamoeba was based on the morphology of cyst and trophozoite forms and PCR amplification with a genus specific primer pair. The pathogenic potential of Acanthamoeba isolates was characterized using PCRs with two primer pairs related to Acanthamoeba pathogenesis and cytotoxicity assays using human corneal cells. Isolates genotypes were also determined after ribosomal DNA sequencing. These data revealed that the potentially pathogenic isolates belonged to T3 and T4. To our knowledge, this is the first report presenting the isolation of potentially pathogenic Acanthamoeba strains in wild squirrels, and it is also the first description of the pathogenic T3 and T4 Acanthamoeba genotypes in Fuerteventura and Morocco.