Samples of Merluccius australis (113 fish) and of M. hubbsi (195 fish) were collected from 16 positions on the Falklands and Argentine shelves and 1 off southern Chile. Twenty-eight fungal, protozoan, and metazoan parasite taxa, of which 19 were identified to the species level, and cysts of unknown etiology, were found. These included one new species of myxosporean protozoan found in both host species, three species that are new to both species of hake, three species not previously reported from M. australis, and one not previously reported from M. hubbsi. The most promising biological tags for stock identification, where long life spans are important, are an unidentified fungus; the protozoans Alatospora merluccii Kalavati, Longshaw and MacKenzie, 1995, Goussia sp., Kudoa rosenbuschi (Gelormini, 1944), Microsporidium ovoideum (Thélohan, 1895), Myxidium baueri Kovaleva and Gaevskaya, 1982, and Myxoproteus meridianalis Evdokimova, 1977; the metacestodes Grillotia sp. and Hepatoxylon trichiuri (Holten, 1802); and the parasitic copepod Trifur tortuosus Wilson, 1917. The adult digenean Elytrophalloides oatesi (Leiper and Atkinson, 1914) showed some potential as a tag for following seasonal migrations of hake.