DNA extracted from 121 samples of cutaneous and mucosal lesions from 23 Indo-Pacific dolphins (Tursiops aduncus), residents of a marine park, over a 6-year period, were assayed for the presence of cetacean alpha- and gammaherpesviruses , cetacean papillomaviruses, and cetacean pox- and parapoxviruses using specific and generic PCR assays that targeted: thymidine kinase gene of alphaherpesviruses, glycoprotein B gene of gammaherpesviruses, major capsid L1 gene of papillomaviruses, DNA polymerase gene of cetacean poxviruses and the major envelope gene of parapoxviruses. Gammaherpesvirus DNA was detected in oral and genital mucosal lesions, but not in cutaneous lesions, strongly suggesting that these infections are sexually transmitted. Lesions containing gammaherpesvirus DNA were detected over several years in 43 of the 121 samples and may indicate a state of constant productive infection. Sequencing of the glycoprotein B ORF of 3 gammaherpesvirus-containing lesions revealed the presence of a single gammaherpesvirus species. Alphaherpesvirus infection was not demonstrated in any of the mucosal or skin lesions assayed. Infections with papillomaviruses seemed transient, persisting only for a few weeks, and were detected in 9 (7 mucosal and 2 skin lesions) of the samples. Five of the 7 oral and genital mucous membrane lesions contained both a papillomavirus and a gammaherpesvirus. In one dolphin, 2 different papillomaviruses were detected in a skin and a vaginal lesion sampled at the same time. Sequencing of the major capsid L1 ORF of the 9 papillomavirus positive samples showed that their identity ranged from 82.2 to 99.6%, indicating the presence of more than one papillomavirus genotype. No evidence of infection with cetacean pox- or parapoxviruses was found in any of the lesions tested, indicating that this closed population of dolphins is, most likely, free of those infections. In summary, a single gammaherpesvirus species was associated with persistent lesions in the mucous membranes, both oral and genital in dolphins of this marine park, while papillomaviruses of various genotypes were responsible for transient infections in both cutaneous and mucous membrane lesions.