Time/area closures have been widely used in fisheries management to prevent overfishing and the destruction of marine biodiversity. To a lesser degree, such spatio-temporal management measures have been used to reduce by-catch of finfish or protected species. However, as ecosystem-based management approaches are employed and more fisheries are managed through multispecies, multiobjective models, the management of by-catch will likely become increasingly important. The elimination of by-catch has become a primary goal of the fishing policies of many countries. It is particularly relevant in the United States, as the deadline for setting annual catch limits (ACLs) in all fisheries passes in 2011. This will result in a dramatic expansion of the number of catch and by-catch quotas. Such catch measures may result in the early closure of otherwise sustainable fisheries when by-catch quotas are exceeded. To prevent such closures and the consequent economic hardship to fishers and the economy, it is imperative that managers be given the tools necessary to reduce by-catch and improve fishing selectivity. Targeted spatio-temporal fishery closures are one solution open to managers. Here, we examine how the spatio-temporal and oceanographic characteristics of by-catch may be used by managers to design fishery closures, and place these methods within a decision tree to assist managers to identify appropriate management measures. We argue that the current movement towards marine spatial planning (MSP) presents an important impetus to examine how we manage fisheries spatially, and we offer a first step towards the objective participation of fisheries in the MSP process.