Developing methods to effectively survey small, nocturnal mammals is important for conservation and management, as they are prey for many other species, including those of conservation concern, and may be threatened or endangered themselves. The Humboldt's Flying Squirrel (Glaucomys oregonensis), previously thought to be part of the Northern Flying Squirrel species (Glaucomys sabrinus), was recently discovered to be a separate species. The ability to effectively and efficiently survey for this species will be essential to evaluating its conservation status. Here we test a non-invasive method to survey for Humboldt's Flying Squirrels by using baited camera traps in old-growth and second-growth Coastal Redwood (Sequoia sempervirens) forests in northwestern California. We found that the camera trap method was successful at detecting flying squirrels in both stand types; however, the number of detections and activity levels were greater in the old-growth forest. Humboldt's Flying Squirrels may prefer old-growth forest when it is available, but still appear to utilize some second-growth forest stands. Camera traps can be used instead of live trapping when researchers or land managers are interested in determining the presence or absence of Humboldt's Flying Squirrels in forested habitat.