In heterogeneous landscapes, habitat preference constitutes a crucial link between landscape and population-level processes such as density and sex ratios. We conducted a non-invasive genetic study of white-tailed deer in southern Finland using fecal samples. We estimated deer density as a function of landcover type using a Spatial Capture-Recapture (SCR) model. Second-order habitat selection of white-tailed deer revealed particularly high densities in fields and mixed forest, and third-order selection was related to distance to fields and transitional woodlands (clearcuts). Including landscape heterogeneity improved model fit compared with assuming a homogenous landscape. Our findings underline the importance of including habitat covariates when estimating density.