In response to over-exploitation and ecosystem degradation, United States federal fisheries policy is shifting from species-based to ecosystem-based management. In addition, the reauthorized Magnuson-Stevens Fisheries Conservation and Management Reauthorization Act of 2006 identifies the following goals to be achieved by 2011: end over-fishing, create market-based incentives, strengthen enforcement mechanisms, and improve cooperative conservation efforts. We refer to these goals (including the “status quo”) as front-ended policy objectives. Left unresolved are what we term back-ended policy and legal issues, specifically including issues involving the legal limitations that inhibit full consideration of ecosystem-based management principles through the adopting of scientific information. In this paper, we identify and examine some of these legal limitations, including the standard of review used in judicial proceedings. In addition, we also suggest some potential solutions to these major governance obstacles. We believe the ultimate value of this paper is the identification of recurring framework issues in United States fisheries management if, left unresolved, will continually limit the conservation-related goals such as those identified in the Magnuson-Stevens Fisheries Conservation and Management Reauthorization Act of 2006. As such, these legal obstacles should be a primary focus of policy makers who wish to achieve fishery conservation goals in-line with scientific research.