In dogs, papillomaviruses are thought to cause oral and cutaneous papillomas and pigmented plaques. Eight canine papillomaviruses have been fully sequenced to date. Four of these canine papillomaviruses, including Canis familiaris papillomavirus (CPV)-3, CPV-4, CPV-5, and CPV-8, were amplified from pigmented plaques. Given the identification of several different canine papillomaviruses within pigmented plaques, it is likely that there are additional papillomavirus sequences that have not been previously identified. The aim of the present study was to amplify papillomavirus DNA from pigmented plaques and identify potentially novel papillomavirus sequences through nucleotide sequence analysis. Polymerase chain reaction was used to amplify DNA sequences of the papillomavirus L1 gene from 27 pigmented plaques. Identification of novel papillomavirus sequences was based on less than 90% shared DNA homology to any known papillomavirus. DNA from 10 different papillomaviruses was identified within the pigmented plaques, including 6 putative novel papillomavirus sequences. CPV-4 was detected within 41% (11/27) of the pigmented plaques, while CPV-5 was identified within 2 pigmented plaques and CPV-3 within a single pigmented plaque. A previously identified novel papillomavirus sequence was identified within 2 pigmented plaques. The remaining 11 pigmented plaques contained 6 papillomavirus DNA sequences that have not been previously reported. These putative novel PV sequences were most similar to the canine papillomaviruses that have been detected within canine pigmented plaques.