Land ownership in Alaska includes a mosaic of federally managed units. Within its agency’s context, each unit has its own management strategy, authority, and resources of conservation concern, many of which are migratory animals. Though some units are geographically isolated, many are nevertheless linked by paths of abiotic and biotic flows, such as rivers, air masses, flyways, and terrestrial and aquatic migration routes. Furthermore, individual land units exist within the context of a larger landscape pattern of shifting conditions, requiring managers to understand at larger spatial scales the status and trends in the synchrony and spatial concurrence of species and associated suitable habitats. Results of these changes will determine the ability of Alaska lands to continue to: provide habitat for local and migratory species; absorb species whose ranges are shifting northward; and experience mitigation or exacerbation of climate change through positive and negative atmospheric feedbacks. We discuss the geographic and statutory contexts that influence development of ecological monitoring; argue for the inclusion of significant amounts of broad-scale monitoring; discuss the importance of defining clear programmatic and monitoring objectives; and draw from lessons learned from existing long-term, broad-scale monitoring programs to apply to the specific contexts relevant to high-latitude protected areas such as those in Alaska. Such areas are distinguished by their: marked seasonality; relatively large magnitudes of contemporary change in climatic parameters; and relative inaccessibility due to broad spatial extent, very low (or zero) road density, and steep and glaciated areas. For ecological monitoring to effectively support management decisions in high-latitude areas such as Alaska, a monitoring program ideally would be structured to address the actual spatial and temporal scales of relevant processes, rather than the artificial boundaries of individual land-management units. Heuristic models provide a means by which to integrate understanding of ecosystem structure, composition, and function, in the midst of numerous ecosystem drivers.