Five genetically distinct macropodid marsupial herpesviruses have been reported [Macropodid alphaherpesviruses 1 and 2 (MaHV-1 and -2); Macropodid herpesviruses 3 to 5 (MaHV-3 to -5)]. MaHV-2 was originally isolated from an outbreak of fatal disease in captive quokkas (Setonix brachyurus) that were in contact with other macropodid species. This warranted a survey of the presence of herpesviruses in this threatened and endemic Western Australian (WA) wallaby. Blood samples from 142 apparently healthy quokkas were tested for exposure to MaHV-1 and -2 by serology. Of these 142, 121 [Rottnest Island (RI), n = 93; mainland WA, n = 28] were tested for herpesvirus infection by polymerase chain reaction (PCR). Antibodies to MaHV-1 and -2 were detected in one individual [prevalence, 0.7%; 95% confidence interval (CI), 0.1%–3.2%] from the mainland and none from RI. However, a novel gammaherpesvirus [designated Macropodid herpesvirus 6 (MaHV-6)] was detected by PCR in the blood of 13 of 121 individuals (11%; 95% CI, 6.2–17.2). Infection with MaHV-6 was significantly more prevalent on the mainland (7/28; i.e., 25%) compared with RI (6/93; i.e., 6.45%; difference in sample proportions, 95% CI, 6%–32%; P = 0.015). There was no association (P > 0.05) between infection with MaHV-6 and differences in hematology, blood chemistry, peripheral blood cell morphologies, or on clinical status. There was a significant association between infection with MaHV-6 and the presence of Theileria spp. in blood [odds ratio (OR) = 11.0; 95% CI, 2.31–52.3; P = 0.001] and yeast in the nasal lining (OR = 7.0; 95% CI, 1.54–31.8; P = 0.021), suggesting that quokkas may be more susceptible to infection with these microorganisms if also infected with MaHV-6. MaHV-6 infection may be a catalyst for vulnerability to disease with other infectious agents and may pose a significant threat to other macropods. These findings have implications for in situ and ex situ management programs of quokkas.