Populations of Steller sea lions, northern fur seals, and northern sea otters declined substantially during recent decades in the Bering Sea and Aleutian Islands region, yet the population status of harbor seals has not been assessed adequately. We determined that counts obtained during skiff-based surveys conducted in 1977–1982 represent the earliest estimate of harbor seal abundance throughout the Aleutian Islands. By comparing counts from 106 islands surveyed in 1977–1982 (8,601 seals) with counts from the same islands during a 1999 aerial survey (2,859 seals), we observed a 67% decline over the ∼20-yr period. Regionally, the largest decline of 86% was in the western Aleutians (n= 7 islands), followed by 66% in the central Aleutians (n= 64 islands), and 45% in the eastern Aleutians (n= 35 islands). Harbor seal counts decreased at the majority of islands in each region, the number of islands with >100 seals decreased ∼70%, and the number of islands with no seals counted increased ∼80%, indicating that harbor seal abundance throughout the Aleutian Islands was substantially lower in the late 1990s than in the 1970s and 1980s.