According to Eric Branch of the San Francisco Chronicle, the 49ers interviewed Shanahan on Tuesday. The team interviewed Kelly on January 7.
Shanahan has been the head coach of the Los Angeles Raiders, Denver Broncos, and most recently, the Washington Redskins. He was the 49ers offensive coordinator from 1992 through 1994, when they won their last Super Bowl. He won Super Bowls in 1997 and 1998 with the Broncos.
The 49ers met with Shanahan for six hours last year before ultimately deciding to hire Jim Tomsula as their head coach. He is 178-144 as a head coach, including the postseason.
Kelly served as the head coach at the University of Oregon from 2009 to 2012. compiling a 46-7 record. He led the Ducks to two Bowl wins over his college coaching career, winning the 2012 Rose Bowl and the 2013 Fiesta Bowl.
He became the head coach of the Eagles in 2013 and had a 26-22 record before being fired on December 29 following a 6-9 2015 season. However, the Eagles finished with a 10-6 record during each of his previous two seasons.
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