Domestic dogs (Canis familiaris) are frequent visitors to protected areas, but little is known about how they affect wildlife communities. We studied the effects of dogs on wildlife communities by comparing the activity levels of wildlife in areas that prohibited dogs with areas that allowed dogs. We measured wildlife activity on trails and up to 200 m away from trails using five methods: (1) pellet plots, (2) track plates, (3) remote triggered cameras, (4) on-trail scat surveys, and (5) mapping prairie dog (Cynomys ludovicianus) burrow locations. The presence of dogs along recreational trails correlated with altered patterns of habitat utilization by several species. Mule deer (Odocoileus hemionus) activity was significantly lower within 100 m of trails in areas that allowed dogs than in areas that prohibited dogs. Small mammals, including squirrels (Sciurus spp.) and rabbits (Sylvilagus spp.), also exhibited reduced levels of activity within 50 m of trails in areas that allowed dogs when compared with areas without. The density of prairie dog burrows was lower within 25 m of trails in areas that allowed dogs. The presence of dogs also affected carnivore activity. Bobcat (Felis rufus) detections were lower in areas that allowed dogs, and red fox (Vulpes vulpes) detections were higher. These findings have implications for the management of natural areas, particularly those that allow dogs to be off-leash.