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 this recent 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 this study was to detect papillomavirus DNA sequences from pigmented plaques and identify potentially novel PV 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 upon less than 90% shared DNA homology to any known papillomavirus. Ten different papillomaviruses were detected within the pigmented plaques, including 6 novel PV 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 in this study. The remaining 11 pigmented plaques contained 6 papillomavirus DNA sequences that have not been previously reported. These novel PV sequences were most similar to papillomaviruses that have been detected within canine pigmented plaques.