We found a highly divergent circovirus in serum samples from several dogs. Phylogenetic analysis indicates that canine circovirus genotype 1 (CaCV-1) represents the first circovirus reported in dogs and is genetically most closely related to the only known mammalian circovirus, porcine circovirus. Here we report the complete genome sequence of the CaCV-1 strain NY214, which will help toward understanding the evolutionary and pathogenic characteristics of mammalian circoviruses.