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Benoît, H. P. 2013. Two decades of annual landed and discarded catches of three southern Gulf of St Lawrence skate species estimated under multiple sources of uncertainty. – ICES Journal of Marine Science, 70: 554–563. Estimating fishery impacts on commercially unimportant species is often hindered by limited and possibly biased data for landed and discarded catch, and poor information on discard mortality. The three skate (family Rajidae) species occurring in southern Gulf of St Lawrence (Canada) exemplify this problem. Assessing the contribution of fishing to important declines in their adult abundance has been complicated by catch data that are not disaggregated by species, concerns about the reliability of discard amounts estimated from fisheries observer surveys, and unknown discard mortality rates. An approach is presented for producing annual estimates of landed and discarded catch, as well as discard mortality rates, for the three species for the period 1991–2011. The approach used data from landing statistics and from observer surveys, and models for disaggregating mixed fishery catches into their constituent species and for estimating minimum discard mortalities. Bootstrapping was used to propagate errors associated with different components of the estimation process. The estimation was partly validated by comparing recorded landings with landings estimated from fisheries observer surveys. This paper demonstrates how multiple sources of uncertainty in discard loss estimation can be addressed by dividing the estimation process into linked components that can be individually addressed and ideally validated.