Establishment of the Papahānaumokuākea Marine National Monument (PMNM) in 2006 was heralded as a major advance for marine conservation. The PMNM is one of the largest no-take marine reserves in the world (36,207,439 hectares) and includes all of the Northwestern Hawaiian Islands (NWHI). Despite the protection, within its boundaries one of Hawaii's most charismatic marine species, the endemic Hawaiian monk seal (Monachus schauinslandi), is declining towards extinction. In contrast, monk seal abundance is increasing in the largely unprotected Main Hawaiian Islands. High juvenile mortality in the NWHI has been identified as the demographic factor responsible for the population decline. The ecological drivers of the dynamic are unknown. We evaluate an intervention proposed by the Pacific Islands Fisheries Science Center within the PMNM in a situation in which there is little or no precedent of theory to support management decisions, and then examine the conflicting conservation mandates that pose challenges for monk seal conservation. Benefits of intervention include the potential to maintain subpopulations in the NWHI, and therefore preserve the metapopulation structure, and it will provide additional time for management agencies to continue studies to understand factors limiting population growth. If conditions inside the PMNM do not improve, however, juvenile seals will continue to experience poor survival and subpopulations in the NWHI will continue to decline in spite of intervention. The long-term success of any intervention requires the underlying ecological reason for the NWHI population decline, which is currently unclear. The failure of the PMNM to conserve endangered Hawaiian monk seals highlights conflicting goals of different conservation agendas, the need to understand ecosystem function and large-scale ecosystem interactions, and the necessity of adaptive management.