The paper compares the management outcomes with a total allowable catch (TAC) and a total allowable effort (TAE) in a fishery under uncertainty. Using a dynamic programming model with multiple uncertainties and estimated growth, harvest and effort functions from one of the world’s largest fisheries, the relative economic and biological benefits of a TAC and TAE are compared and contrasted in a stochastic environment. This approach provides a decision and modeling framework to compare instruments and achieve desired management goals. A key finding is that neither instrument is always preferred in a world of uncertainty and that regulator’s risk aversion and weighting in terms of expected net profits and biomass and the trade-offs in terms of expected values and variance determine instrument choice.