This study reports the detection of co-infection by multiple CPV variants and the high genetic complexity of a CPV-2 strain detected in a domestic cat. The CPV variants selected by cloning the VP2 gene were sequenced, and genetic diversity and selection pressure were investigated. Comparison of the nucleotide sequences has evidenced 10 different viral populations, and, in the same animal, more CPV variants coexist. Our analysis excludes the possibility that the recombination events took place during infection and that negative selection acted on the VP2 gene. These findings confirm that CPV-2 shows high genetic heterogeneity resembling the quasispecies found in RNA viruses.