This paper evaluates the bioeconomic performance of individual fishing quota (IFQ) regulations in a multiple-species fishery. In our model, fisheries managers face uncertainty over the population sizes and growth characteristics of multiple cohabiting fish species'. Fishers control all aspects of harvest operations under full knowledge of the species-specific productivities of their fishing gear. We derive a rational equilibrium mapping from bioeconomic fundamentals and the IFQ regulation to the private profit maximizing mortality and rent outcomes that are implemented by fishers. Conditional on this mapping, we solve the second best problem of designing the regulation to maximize fishery value. Performance of a design that allows discretion over the mix of harvested species is contrasted against rules, via a discard ban. Both designs eliminate discards. Discretion diminishes information asymmetry between the manager and fishers and raises fishery value. Incorporating discretion into regulatory designs provides new prospects for improving fisheries management.