We estimated trends in abundance of harbor seals (Phoca vitulina richardsii) using over dispersed, multinomial models and counts obtained during aerial surveys conducted during 1983–2001 in the Ketchikan, Sitka, Kodiak, and Bristol Bay areas of Alaska. Harbor seal numbers increased significantly at 7.4%/yr during 1983–1998 and 5.6%/yr during 1994–1998 in the Ketchikan area, and 6.6%/yr during 1993–2001 in the Kodiak area. Counts were stable (trends not significant) during 1984–2001 (0.7%/yr) and 1995–2001 (-0.4%/yr) in Sitka, and during 1998–2001 (-1.3%/yr) in Bristol Bay. The influence of covariates (e.g., survey date, tide height) on trend estimates was significant and varied among areas and across years, demonstrating the need to include covariates in statistical analyses to accurately estimate trend. Our increasing trend estimate for Kodiak represents the first documented increase in harbor seal numbers over a relatively expansive area in the Gulf of Alaska. However, the trend for the Gulf of Alaska stock is equivocal due to the continued decline in Prince William Sound. Similarly, the trend for the Southeast Alaska stock is equivocal based on our increasing (Ketchikan) and stable (Sitka) trend estimates, and a recent decline reported for Glacier Bay. The Bering Sea stock appears stable after a period of possible decline.