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Johnson, 55, spent 12 years in the Red Sox organization and served the last two seasons on former manager Terry Francona's staff.
Johnson joined the Red Sox in 2000 as a manager of Class A Sarasota before moving on to Double-A Portland. He also served as manager of Triple-A Pawtucket from 2005 to 2009 before being named first-base coach for the Red Sox prior to the 2010 season.
Johnson is the first member of Francona's staff to be fired from the team.
Pitching coach Curt Young said he is "on hold" until a new manager is hired.
Johnson left the team in August 2010 and did not return for the remainder of the season after his daughter lost her leg in a near-fatal accident.Joe McDonald covers the Red Sox for ESPNBoston.com.