Understanding patch dynamics can help scientists better understand metapopulations and the relationships of animals that share a habitat. The Burrowing Owl (Athene cunicularia) is a well-known associate of prairie dog colonies, thereby linking conservation measures that benefit these species. We used occupancy modeling to determine how colony attributes (e.g., size and edge effects) and the loss of prairie dog colonies to sylvatic plague affected the occupancy of those colonies by Burrowing Owls in north-central Montana. We surveyed presence–absence of Burrowing Owls during a 13-yr period (1995–2007) and analyzed the data using a robust-design occupancy model in Program MARK. The proportion of colonies occupied by Burrowing Owls ranged from 0.41 to 0.54 across years while the probability of detecting the owls ranged from 0.22 to 0.92. Contrary to our predictions, colony edge effects and plague epizootics showed only weak or no effects on Burrowing Owl occupancy. Prairie dog colony size had the greatest effect on Burrowing Owl occupancy patterns. Colonization of prairie dog colonies by owls generally increased with colony area, whereas owl extinction initially dropped and then increased as a function of increasing colony area. We found no direct link between Burrowing Owl occupancy of prairie dog colonies and plague history, but our results reaffirmed the importance of colony size. Collectively, this information will help inform future conservation efforts for Burrowing Owls that occupy prairie dog colonies.