James Lee DiMaggio, 40, was killed about 4 p.m. in a remote area near the town of Cascade, according to a source familiar with the investigation.
DiMaggio was the subject of an intensive manhunt in the wilderness above Cascade, where he had taken Hannah, who had been missing from her San Diego County community since Sunday.
No other details about how DiMaggio was killed were immediately available.
DiMaggio had been considered armed and dangerous. Earlier in the day, FBI Special Agent Jason Pack said that danger required officials to send in "highly trained, enhanced SWAT teams and law enforcement" as part of the search.
DiMaggio's blue Nissan Versa — the subject of a five-state Amber Alert — was found Friday roughly 60 miles northeast of Cascade, at a trail head leading into the wilderness.
Ada County sheriff's spokeswoman Andrea Dearden said it was "the last place you can go before you hit the wilderness and stop driving."
Much of the terrain is so rugged and remote that some ground search crews had to be flown in Saturday morning. Others took to horseback, while helicopters buzzed overhead.
By Saturday afternoon, roughly 150 FBI officials had combined with local and state officials to amass a force of more than 200 personnel, according to Dearden.
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