Kingston, who was the assistant general manager under previous GM Jack Zduriencik, has been promoted to vice president and assistant GM of baseball operations. Kingston takes on additional duties overseeing the Mariners' player development department.
Kingston has been with the Mariners since 2009 after previously working in the Padres organization.
Allison, who has been the director of pro scouting since 2012, has been promoted to vice president of player personnel. He will now oversee all aspects of the Mariners' scouting operation, including amateur, pro and international departments.
Allison has more than 20 years of pro scouting experience and has previously worked with the Mets, Brewers, D-backs and Red Sox.
MacPhail, who has been working as a Major League scout for the Mariners since 2012, takes over Allison's former role as director of pro scouting. He has previously scouted for the Orioles, Twins, Nationals, Indians and Rangers.
Tom McNamara will continue in his role as director of amateur scouting, and Tim Kissner remains the director of international scouting. Along with MacPhail, they will all report now to Allison.
Bohringer fills one of the spots created when former special assistants to the GM Ted Simmons, Joe McIlvaine and Pete Vuckovich were informed their contracts would not be renewed as of Nov. 1.
Bohringer has been the Cubs' director of pro scouting the past four years after working as a pro scout for the D-backs from 2006-11. He worked for Dipoto during that time in Arizona when Dipoto was the D-backs' director of player personnel from '06-10 and VP of scouting and player development in '11.
Bohringer, a graduate of MIT's Sloan School of Management in 1993, worked for the Mariners as an area scouting supervisor from 2002-06 in California and then the Midwest.
Dipoto had previously announced the hiring of Rockies sports psychologist Andy McKay as the team's director of player development, replacing former farm director Chris Gwynn, who resigned on Oct. 8.