Invasions by non-indigenous species are amongst the greatest threats to global biodiversity, causing substantial disruption to, and sometimes local extinction of, individual species and community assemblages which, in turn, can affect ecosystem structure and function. The terrestrial environment of Antarctica consists of many isolated ‘islands’ of ice-free ground. Prolonged isolation makes Antarctic biodiversity vulnerable to human-mediated impacts, in particular (1) the introduction of non-indigenous species from outside Antarctica, and (2) the redistribution of indigenous Antarctic species between biologically distinct areas within the continent. The Protocol on Environmental Protection to the Antarctic Treaty, the primary instrument through which environmental management is addressed within the Antarctic Treaty System, says little about unintentional introduction of non-indigenous species to Antarctica, and nothing specifically about human-mediated transfer of native species from one area to another. We review the effectiveness of the Antarctic protected area system, the primary means through which area-specific environmental protection is achieved under the Antarctic Treaty System. This reveals that the measures described in most Antarctic Specially Protected Area (ASPA) and Antarctic Specially Managed Area (ASMA) Management Plans, by themselves, may not be sufficient to (1) minimise the possibility of introduction of plants, animals and microbes not native to the protected area or (2) adequately protect the many unusual assemblages of species, type localities or only known habitats of certain species found in Antarctica. We discuss issues that should be considered in the development of a more effective system, including the implementation of appropriate biosecurity measures across different spatial scales and applied to different biological groups.