Acanthamoeba spp. are free-living amoebae that are ubiquitously distributed in the environment and can cause encephalomyelitis in animals and humans. The factors that contribute to Acanthamoeba infections include parasite biology, genetic diversity, environmental spread, and host susceptibility. The aim of the present study was to characterize isolates of Acanthamoeba from the nasal mucosa and cutaneous lesions of dogs in order to access the occurence and pathogenicity of these organisms in this animal group. We studied 13 isolates of Acanthamoeba confirmed by polymerase chain reaction. They were sequenced, the genotype was determined, and their potential of pathogenicity was evaluated.