Densely vegetated environments have hindered collection of basic population parameters on forest-dwelling ungulates. Our objective was to develop a mark—recapture technique that used DNA from fecal pellets to overcome constraints associated with estimating abundance of ungulates in landscapes where direct observation is difficult. We tested our technique on Sitka black-tailed deer (Odocoileus hemionus sitkensis) in the temperate coastal rainforest of Southeast Alaska. During 2006–2008, we sampled fecal pellets of deer along trail transects in 3 intensively logged watersheds on Prince of Wales Island, Alaska. We extracted DNA from the surface of fecal pellets and used microsatellite markers to identify individual deer. With genotypes of individual deer, we estimated abundance of deer with moderate precision (±20%) using mark—recapture models. Combining all study sites, we identified a 30% (SE = 5.1%) decline in abundance during our 3-year study, which we attributed to 3 consecutive severe winters. We determined that deer densities in managed land logged >30 years ago (7 deer/km2, SE = 1.3) supported fewer deer compared to both managed land logged <30 years ago (10 deer/km2, SE = 1.5) and unmanaged land (12 deer/km2, SE = 1.4). Our study provides the first estimates of abundance (based on individually identified deer) for Sitka black-tailed deer and the first estimates of abundance of an unenclosed ungulate population using DNA from fecal pellets. Our tool enables managers to accurately and precisely estimate the abundance of deer in densely vegetated habitats using a non-invasive approach.