Elucidating the differential use of resources by animals is fundamental to both understanding ecological processes and making informed conservation decisions. Such information is particularly important for poorly studied species that may be dependent upon heavily exploited resources. We examine habitat selection of the Northern Pygmy-Owl (Glaucidium gnoma), which is thought to depend upon mature forests, but for which information on habitat use is scant. We conducted our study in northern Idaho and western Montana, and used the synoptic model of space use. We obtained sufficient location data to include 27 radio-tagged owls in the study (16 in Idaho and 11 in Montana). To evaluate habitat selection, we developed 36 models in Idaho and 24 models in Montana, each with different combinations of habitat covariates hypothesized to influence Northern Pygmy-Owl space use. Covariates representing larger tree size were statistically significant ( ≥ 3.01, t ≥ 2.7, P ≤ 0.02) predictors of space use in the best-supported population-level models in both Idaho and Montana. In addition, the distance-to-stream covariate was a statistically significant ( = −3.60, t = −3.3, P = 0.005) predictor of the probability of use in the best-supported population-level model in Idaho, but not in the best-supported Montana model ( = −0.08, t =0.03, P = 0.98). Owls selected forested areas with larger tree sizes and (in Idaho) selected areas closer to stream courses. Differences between the two study areas in the apparent importance of stream proximity to habitat selection may reflect differences in timber harvest practices and the amount of coniferous vegetation; however, this hypothesis should be addressed with additional research.