Kodiak is also home to large numbers of marbled murrelets, a secretive seabird that nests on the massive moss covered limbs of old-growth trees and occasionally on the ground. Kittlitz’s murrelet, a close relative of the marbled murrelet, were recently discovered nesting on scree and talus slopes at relatively high elevation on Kodiak Refuge. This species has since become the focus of a major nesting ecology study conducted by the US Fish and Wildlife Service in partnership with the USGS Alaska Science Center, and Oregon State University.

One of the most ubiquitous and conspicuous birds on Kodiak is the majestic bald eagle, which is resident year round on the island. The numbers of breeding bald eagles have steadily increased since the 1960s and have now stabilized on the Refuge, and eagles can be seen in large numbers in downtown Kodiak in the winter.

Species of concern such as emperor geese and Steller’s eiders are commonly encountered in the bays around Kodiak along with other wintering migrants. The Steller's eider is the smallest of the eiders, and the species has been listed as threatened on the Federal Register since 1997.