Papillomavirus (PV) DNA is frequently uncovered in samples of human skin squamous cell carcinomas (SCC). However, the role of these viruses in the development of such cancers in canine species remains controversial. While approximately 100 human PVs are known, only one single canine oral PV (COPV) has been identified and studied extensively. Therefore, we applied a narrow-range polymerase chain reaction (PCR) suitable for the detection of classical canine and feline PVs, as well as a broad-range PCR, which has been used for the detection of various novel PVs in humans, in order to analyse 42 paraffin-embedded samples, representing three different forms of canine SCCs. Ten samples of skin tissues with various non-neoplastic conditions served as controls. While none of the negative controls reacted positively, PV DNA was discovered in 21% of the tested SCC samples. Interestingly, the classical COPV was amplified from only one sample, while the other positive cases were associated with a variety of thus far unknown PVs. This study suggests that a fraction of canine SCC is infected with PVs and that a genetic variety of canine PVs exists. Therefore, these results will facilitate the future study of the role of PVs in the development of canine skin cancers.