Murphy, who was a special assistant in the front office last season, has won 1,000 games at the collegiate level and was the head coach at Arizona State from 1995-2009.
The Padres announced their coaching staffs for their Minor League affiliates Tuesday.
Terry Kennedy will return for his second season as manager of the Padres' Triple-A team, which will be in Tucson in 2011. The team had previously played in Portland, Ore.
Kennedy, a former All-Star catcher for the Padres, will be joined in Tucson by pitching coach Steve Webber and Bob Skube, who will be the hitting coach.
Doug Dascenzo will return as manager of the Double-A San Antonio Missions. Dascenzo led Class A Fort Wayne to the Midwest League championship in 2009. Dascenzo will be joined by Jimmy Jones (pitching coach) and Tom Tornincasa (hitting coach).
Carlos Lezcano will begin his fifth season at the manager of the Padres' Class A Advanced affiliate in Lake Elsinore, Calif. Bronswell Patrick will be the pitching coach for the Storm and Phil Plantier will be the hitting coach. Plantier was the Mariners' roving hitting coordinator in 2010.
Shawn Wooten will be the manager at low Class A Fort Wayne, making the jump from the hitting-coach position with short-season Eugene. Willie Blair will be the pitching coach in Fort Wayne and Kory DeHaan will be the hitting coach.
Joining Murphy in Eugene will be pitching coach Dave Rajsich and hitting coach Chris Prieto.
The Rookie-level team in Arizona will be managed by Jim Gabella in 2010. Gabella spent the last seven seasons managing in the Royals organization. Nelson Cruz will be the pitching coach and Ivan Cruz will be the hitting coach. Tim Worrell will serve as the rehabilitation pitching coach.
Evaristo Lantigua remains as the coordinator of Latin American instruction/field manager of the Rookie-level Dominican Summer League team. Jose Amancio will return as the pitching coach as will hitting coach Christian Reyes.
The Padres also named their Minor League roving instructors: Randy Johnson (field coordinator), Mike Couchee (pitching coordinator), Sean Berry (hitting coordinator), Gary Jones (infield coordinator) and Glen Barker (outfield/baserunning coordinator).