Second season, Episode 9
Owls can represent both wisdom and evil. In Twin Peaks, owls appear whenever UFO sightings are made. Owls are frequently mentioned in old Indian tales. Owls are first mentioned in Episode 1 from the second season. One of the three things "The Giant" tells Cooper is, "The owls are not what they seem." Cooper has yet to find out what that means.
What we do know is that on July 25, 1986, Laura Palmer was almost killed by an owl. Laura frequently was frightened by the owls she saw in the woods. In Episode 9, after BOB vacated Leland's body, the last scene is of an owl flying.