Commercial fisheries in the United States are managed by eight regional fisheries management councils operating under the authority of the National Marine Fisheries Service (NMFS, Department of Commerce) and governed by the Magnuson-Stevens Fisheries Conservation and Management Act and accompanying federal guidelines. The Act mandates that NMFS identify essential fish habitat (EFH) for fish stocks and minimize, to the extent practicable, adverse effects to EFH through the councils’ fishery management plan development and revisions process. The statute and regulatory guidelines implicitly assume that NMFS and councils have the scientific information necessary to make informed EFH designations for all commercially harvested species, assess the realized or potential threats to EFH, and have the management tools to protect EFH. Further, the interpretation and implementation of several important, but ambiguous, terms in the guidelines are left to NMFS and the councils. Our thesis is that these factors (specifically, insufficient information support and regulatory ambiguities) can and are resulting in inconsistent and potentially sub-optimal fish habitat management throughout the country. As we enter an era of increased climate variability these factors may be having a disproportionally high impact in higher latitudes where change is expected to be more rapid. Here we provide a brief history of essential fish habitat regulations, explain the issues arising from the state of the science and regulatory ambiguities, and conclude with a discussion of the implications and recommendations for United States high latitude EFH management.