Abstract Marine scientists and policymakers are encouraging ecosystem-based fishery management (EBFM), but there is limited guidance on how to operationalize the concept. We adapt financial portfolio theory as a method for EBFM that accounts for species interdependencies, uncertainty, and sustainability constraints. Illustrating our method with routinely collected data available from the Chesapeake Bay, we demonstrate the gains from taking into account variances and covariances of gross fishing revenues in setting species total allowable catches. We find over the period from 1962–2003 that managers could have increased the revenues from fishing and reduced the variance by employing EBFM frontiers in setting catch levels.