Chinook salmon (Oncorhynchus tshawytscha) populations have experienced widespread declines in abundance and abrupt shifts toward younger and smaller adults returning to spawn in rivers. The causal agents underpinning these shifts are largely unknown. Here we investigate the potential role of late-stage marine mortality, defined as occurring after the first winter at sea, in driving this species' changing age structure. Simulations using a stage-based life cycle model that included additional mortality during after the first winter at sea better reflected observed changes in the age structure of a well-studied and representative population of Chinook salmon from the Yukon River drainage, compared with a model estimating environmentally-driven variation in age-specific survival alone. Although the specific agents of late-stage mortality are not known, our finding is consistent with work reporting predation by salmon sharks (Lamna ditropis) and marine mammals including killer whales (Orcinus orca). Taken as a whole, this work suggests that Pacific salmon mortality after the first winter at sea is likely to be higher than previously thought and highlights the need to investigate selective sources of mortality, such as predation, as major contributors to rapidly changing age structure of spawning adult Chinook salmon.