Carnivore protoparvovirus 1 is one of the most important pathogens affecting both wild and domestic carnivores. Here, we reported the genetic characterization of canine parvovirus strains from a rescued guiña (Leopardus guigna) and domestic dogs from Chile. Guiña sequence was classified as CPV-2c and phylogenetic analysis of the complete coding genome showed that the guiña CPV-2c strain share a recent common ancestor with Chilean domestic dogs strains. These viruses presented >99% identity and showed three changes in the NS1 protein, CHL-17 V596A, CHL-71 E661K and CHL-guigna L582F. This is the first detection and genetic characterization of CPV-2c infection in guiña worldwide and one of the few comparative studies that undoubtedly determine that the source of infection were domestic dogs. The current findings highlight that guiña is a susceptible species to protoparvovirus infection and that domestic dogs represent an important thread to its conservation. The CPV cross-species transmission between domestic dogs and guiña should be taken into account for protection programs of this endangerous species.