Informed management of wildlife populations requires the accurate estimation of abundance, sex ratio, and other population parameters. For deer (Odocoileus spp.), the use of closed‐population, capture‐recapture (CR) methods, in conjunction with noninvasive DNA sampling, has become increasingly practical, but, up to now, these methods have been used in a non‐spatial modeling framework, which has limited their utility for population‐level inferences. In particular, extrapolation of plot‐level CR abundance estimates to the population required the use of multipliers of unknown reliability and potential bias. Spatially explicit capture‐recapture (SCR) models provide an integrated framework for directly estimating density as a function of spatial and habitat variables at landscape scales. We used fecal DNA samples in conjunction with SCR to estimate density, sex ratio, and habitat correlates to density for a mule deer (O. hemionus) population across a large (∼500 km2) area in the central Sierra Nevada Range, California, USA during 2013 and 2014. We surveyed 24 random transects within 4 30‐km2 sites representative of the study area. Based on 411 samples genotyped at a sex marker and 8–10 microsatellite loci, the sex‐ratio for the study area was 62 (95% CI = 41–93) males/100 females in 2013 and 65 (95% CI = 45–94) males/100 females in 2014. Using SCR, we estimated density at 5.0 (95% CI = 2.3–7.8) deer/km2 in 2013 and 5.1 (95% CI = 3.1–7.2) deer/km2 in 2014. In comparison, non‐spatial CR analysis produced density estimates on average 60% higher, likely reflecting bias resulting from use of the commonly employed mean maximum recapture distance (MMRD) to estimate effective sampling area. The SCR models indicated that density was effectively homogeneous throughout the study area, with no strong relationship to habitat correlates. Altogether, these results demonstrate the utility of noninvasive fecal DNA methods in a SCR framework for estimation of abundance and density in deer populations at landscape scales. © 2017 The Wildlife Society