Canine parvovirus (CPV) is a highly contagious viral disease that affects dogs, especially puppies. CPV-2 is recognized for its resilience in contaminated environments, ease of transmission among dogs, and pathogenicity for puppies. In this protocol, we have adapted the methodology to allow the recovery of complete CPV-2 genomes directly from clinical samples (dry swabs) from puppies with clinical signals of viral enteritis. A multiplex PCR was designed with primers targeting fragments of 400 to 1,000 base pairs (bp) along the full length of the viral genome. The resulting reads were compared after sequencing with the Nanopore technology. Genome assembly revealed that the smaller fragments generated larger numbers of reads, allowing a more reliable coverage of the genome than those attained with primers targeting larger amplicons. Both new methodologies were efficient in amplification and sequencing.