Bowenoid in situ squamous cell carcinoma (BISC) is a rare feline skin disorder, which has been described as often associated with papillomavirus infection. It is clinically characterized by solitary or multiple hyperkeratotic plaques affecting older cats. Papillomavirus (PV) sequences amplified from feline viral plaques, and BISC lesions seldom correspond to FdPV1. The goal of the present study was to investigate three cases of BISC and to carry out initial genomic analysis of the associated viral DNA. Samples of skin biopsies taken from three BISC cats were histologically characterized. DNA was extracted and rolling-circle amplification was performed on the skin samples. Restriction enzyme analysis of the amplified DNA revealed the presence of a putative unknown PV. The whole genome was subsequently sequenced and cloned. Alignments with previously described feline PV sequences were carried out and phylogenetic trees were generated. The circular 7899 base pair sequence of Felis domesticus PV type 2 (FdPV2) contains a typical noncoding region and characteristic open reading frames (ORF) for six putative viral proteins. Phylogenetic analysis based on the nucleotide alignment of L1 genes or the amino acid alignment of E1 proteins of FdPV2 and 52 other PV types indicates that FdPV2 might represent a new genus.