Stock assessments rely on estimates of total mortality resulting from fishing activities. However, fish that are captured by fishing gear that is not subsequently retrieved are generally not counted in estimates of total fishing removals or otherwise accounted for in stock assessment models. The mortality resulting from the loss of sections of bottom longline gear in the Ross Sea region and Subarea 88.2 Antarctic toothfish (Dissostichus mawsoni) fisheries is not currently known. A method to estimate unaccounted fishing mortality from lost lines in these fisheries is provided. These estimates suggest that on average 208 tonnes of Antarctic toothfish mortality may be unaccounted for annually. While the current estimates may be improved through the adoption of better data reporting practices, these estimates were incorporated as sensitivity analyses in the 2011 stock assessments for the Ross Sea region and Subarea 88.2 toothfish fisheries.