Abstract We report the first confirmed case of toxoplasmosis in an Australian pinniped. Presence of Toxoplasma gondii DNA was detected in the brain of a free-ranging subadult New Zealand fur seal (Arctocephalus forsteri) with nonsuppurative meningoencephalitis, hypophysitis, posterior uveitis, retrobulbar cellulitis, and myocarditis associated with protozoan cysts and tachyzoites. The emaciated seal stranded moribund on a beach in northern Sydney in New South Wales. Histopathology coupled with specific immunohistochemistry and PCR assays confirmed the presence of T. gondii. The T. gondii sample (NZfs8825) identified in this study has an identical genotype as the type II (ToxoDB PCR-RFLP genotype #1) based on the direct sequencing and virtual RFLP of multilocus DNA markers including SAG1, 5′- and 3′-SAG2, alt.SAG2, SAG3, BTUB, GRA6, c22-8, c29-2, L358, PK1, and Apico. Direct sequencing of T. gondii B1 DNA marker from the T. gondii sample (NZfs8825) identified a type II-like strain, based on presence of non-archetypal B1 gene polymorphisms previously reported as unique to Australia. This study suggests that T. gondii oocysts originating from mainland Australia, which has a large population of feral cats, may act as a disease threat to native marine fauna. Therefore, emerging toxoplasmosis in the Arctic has a relevant parallel in the Southern Ocean within Australian waters with yet unknown relevance to Antarctica.