We investigated predation by nonnative coyotes (Canis latrans) on endemic Olympic marmots (Marmota olympus) in Olympic National Park, Washington, in 2005 and 2006. Although nearly the entire marmot range is protected within the park, declines and local extirpations of the species have been documented. Through analyses of carnivore scat across the range of the Olympic marmot we determined the distribution and relative density of coyotes and characterized the extent to which coyotes and native carnivores preyed on marmots. We used mitochondrial DNA analysis of scats to determine carnivore species, and microsatellite markers for individual coyote identification. Scat analysis indicated that invasive coyotes are widespread and the numerically dominant carnivore on sampled trails within the Olympic highlands—71% (301 of 426) of all scats verified to species arose from coyote. Out of all carnivore scats collected, 11.6% (111 of 958) contained marmot remains. For 85% of the samples with marmots, coyotes were confirmed as the predator. The remainder arose from bobcat (13%) and cougar (2%). Coyotes were the predominant marmot predator across all months and in most regions of the park. Twelve out of 13 coyote individuals identified with genetic markers preyed on marmots. Marmots ranked 5th in frequency of coyote diet items, after snowshoe hares (Lepus americanus), mountain beavers (Aplodontia rufa), voles, and cervids. Scat analysis indicated that in the Olympic Mountains, the coyote as an invasive generalist predator is subsidized by abundant multiple prey, and appears to be the primary terrestrial predator on the endemic Olympic marmot. We conclude that predation by coyotes on marmots is widespread and substantial across the marmot's species range, and therefore likely driving observed marmot declines and extinctions.