This paper considers the problem of multi-species fisheries management when targeting individual species is costly and at-sea discards of fish by fishermen are unobserved by the regulator. Stock conditions, ecosystem interaction, technological specification, and relative prices under which at sea discards are acute are identified. A dynamic model is developed to balance ecological interdependencies among multiple fish species, and scope economies implicit in a costly targeting technology. Three regulatory regimes, species-specific harvest quotas, landing taxes, and revenue quotas, are contrasted against a hypothetical sole owner problem. An optimal plan under all regimes precludes discarding. For both very low and very high levels of targeting costs, first best welfare is close to that achieved through any of the regulatory regimes. In general, however, landing taxes welfare dominate species-specific quota regulation; a revenue quota fares the worst.