Measuring the productivity of vessels in a multi-species fishery can be problematic. Typical regression techniques are not capable of handling multiple outputs while Data Envelopment Analysis (DEA) tends to ignore the stochastic nature of production. Applied economists have devoted considerable time to this problem and have developed several methods of dealing with the issue of multiple output technologies in commercial fisheries. Our paper contributes to this literature by providing another method for estimating production functions of vessels operating in multi-species fisheries. We utilize a two-stage model – with data from the West Coast Limited Entry Groundfish Trawl Fishery – using DEA to aggregate output in the first stage. This aggregate index is then used as the dependent variable in a regression framework, allowing for the estimation of the return to different inputs in fisheries production. This provides information that may be particularly important for fisheries managers.