Monitoring of rare and declining species is one of the most important tasks of wildlife managers. Here we present a large-scale, long-term monitoring program for Olympic marmot (Marmota olympus) throughout its range across a logistically challenging mountainous park. Our multiple-stage process of survey design accounts for the difficulty imposed by access to remote habitats and funding constraints. The Olympic marmot is endemic to the Olympic Mountains, Washington State, USA. Although nearly all of its range is enclosed within Olympic National Park, declines and local extirpations of the species have been documented. We considered several possible alternative survey approaches, and propose a monitoring program designed to reflect extinction–recolonisation dynamics using presence–absence data. The sampling design is based on annual surveys of a set of at least 25 randomly selected clusters (closely located groups of sites with record of current or historical occupancy by marmots), and supplemented by sampling 15 never-occupied sites to test for new colonisations. The monitoring plan provides a framework that park managers can use for assessing changes over time in Olympic marmot distribution across the range of the species. Our sampling design may serve as a useful case study for establishing monitoring programs for other species with clumped distributions.