The following 12 players remain from the previous regime.
- Arik Armstead (drafted by the 49ers in 2015, round 1)
- DeForest Buckner (drafted in 2016, round 1)
- Ronald Blair (drafted in 2016, round 5)
- Aaron Burbridge (drafted in 2016, round 6)
- Garrett Celek (undrafted FA in 2012)
- Joshua Garnett (drafted in 2016, round 1)
- Raheem Mostert (undrafted in 2015)
- Kyle Nelson (undrafted in 2011)
- Bradley Pinion (drafted in 2015, round 5)
- Joe Staley (drafted in 2007, round 1)
- Jaquiski Tartt (drafted in 2015, round 2)
- Jimmie Ward (drafted in 2014, round 1)
Lynch and Shanahan inherited 31 of Trent Baalke's draft picks, per Eric Branch of the San Francisco Chronicle. 23 of those players are no longer on the roster. Of those 23, five were traded, seven became free agents, and 11 were waived or released.
Tackle Joe Staley, a 12-year veteran, is the lone player remaining from the pre-Baalke era. He was part of a draft conducted by Scot McCloughan.
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