Killer whale (Orcinus orca) and sperm whale (Physeter macrocephalus) depredation (whales removing or damaging fish caught on fishing gear) can reduce catch rates and decrease the accuracy of fish stock assessments. This study advances our understanding of the impact of whale depredation on the commercial sablefish (Anoplopoma fimbria) fishery in Alaska and evaluates the impact depredation may have on the annual federal sablefish assessment. A statistical modelling approach was used to estimate the whale effect on commercial sablefish fishery catch rates; killer whale depredation was more severe (catch rates declined by 45%–70%) than sperm whale depredation (24%–29%). Total estimated sablefish catch removals 1995–2014 ranged from 1251 t to 2407 t by killer whales in western Alaska management areas and 482 t to 1040 t by sperm whales in the Gulf of Alaska 2001–2014. Including sablefish mortality due to whale depredation on the commercial fishery in the sablefish stock assessment resulted in a 1% reduction in the recommended quota. Accounting for sablefish mortality due to whale depredation in the commercial fishery in the sablefish assessment will occur tandem with correcting for depredation on the annual National Marine Fisheries Service longline survey, the primary survey index used in the assessment.