Twenty years after its adoption, the Convention on the Conservation of Antarctic Marine Living Resources (CCAMLR) remains unique among fisheries agreements in its declared commitment to considering the impact of existing or proposed fisheries on the entire ecosystem, rather than on just the harvested species. However, the recent picture of fisheries activities within the Convention area suggests a substantial – and perhaps widening - gap between theory and practice. The fishery that has most clearly proved beyond CCAMLR’s capacity, and which has posed the most significant environmental damage on the Antarctic environment in modern times, is that for Patagonian Toothfish, Dissostichus eleginoides. That fishery is discussed below, but the roots of that problem (and the structural problems that have contributed to CCAMLR’s inability to deal with the toothfish challenge) threaten to be repeated in the second-generation krill fishery that is rapidly developing Antarctic waters. The authors provide suggestions for structural and procedural changes within CCAMLR to permit it to effectively manage the marine living resources of the Southern Ocean.