Habitat selection has long been viewed as a multi-scale process. Observed species responses to resource gradients are influenced by variation at the scale of the individual, population, metapopulation, and geographic range. Understanding how species interact with habitat at multiple levels presents a complete picture of an organism and is necessary for conservation of endangered species. The main goal of this dissertation is to evaluate distribution, relative abundance, and habitat selection of a rare species, the pygmy rabbit Brachylagus idahoensis, at multiple scales in order to improve management and conservation for this species. At the broadest scale, pygmy rabbit occurrence and relative abundance were modeled in the Duck Creek allotment of northern Utah using a hierarchical spatial model. Pygmy rabbits are not easily observable, and the model used two levels of indirect detection to make statistically rigorous spatial predictions. We found that the model predicted the general pattern of rabbit occurrence and abundance within the study area, and that there was spatial heterogeneity in the probability of pygmy rabbit occurrence within a study domain that was known to be occupied. The resulting model framework could be used to develop a long-term monitoring program for pygmy rabbits and other species for which hierarchically nested levels of indirect observation are collected. The mid-scale analysis evaluated pygmy rabbit home range placement and movement with respect to sagebrush removal treatments using null models based on an optimal central place foraging behavior. While placement of home-range centers did not appear to be affected by the treatments, within-home range movements were farther from treatments than expected by the null models for two rabbits (of eight), and rabbits that approached treatment edges were less likely to enter treatments than expected by chance. Rabbits are not extirpated from sites that have been treated, but the observed reluctance to enter treated patches calls for caution when conducting sagebrush removal treatments near occupied pygmy rabbit burrows. At the finest level of resolution, the spatial ecology of pygmy rabbit use of burrows was evaluated. Both the placement of burrows in general and pygmy rabbit use of burrows were clustered. While the habitat gradients experienced by each of the rabbits evaluated affected the modeled habitat selection responses, some generalities were observed. Selection of high cover suggests that pygmy rabbit use of burrows may be linked to predator avoidance behavior. Additionally, pygmy rabbit use of clustered burrows affects management actions including: habitat modeling, monitoring, and species introduction. Explicit attention to resource distribution will improve efforts to predict species responses to management actions.