Amaro's first assignment will be to represent the Phillies at the annual General Managers Meetings, which begin Monday in Dana Point, Calif. After that, he'll have to figure out which free agents to pursue, and how to manage a budget that is expected to increase from 2008's $104 million.
Pitcher Jamie Moyer and outfielder Pat Burrell are the team's key free agents, and both have expressed an interest to return.
Assistant general manager of scouting and player development Mike Arbuckle, 58, who has been with the team since 1992, won't return next season. It remains to be seen if others will leave with him.
When reached by phone on Sunday, Arbuckle declined to comment.
As the club's assistant general manager, Amaro long has been speculated as the person who would succeed the 71-year-old Gillick, who was hired, in part, to mentor Amaro. Gillick's contract expired Oct. 31.
Amaro, 43, served as a bat boy for the Phillies from 1980-83 and played for the Phillies from 1992-93 and 1996-98. He moved to the front office after retiring as a player. A graduate of Stanford University, Amaro has been heavily involved in many aspects of baseball operations in recent years, including contract negotiations.
Arbuckle's departure is a significant loss for the organization. Under his watch, he and scouting director Marti Wolever supervised Drafts that secured Burrell, Cole Hamels, Ryan Howard, Ryan Madson, Brett Myers, Jimmy Rollins and Chase Utley, while also signing players like Carlos Ruiz out of Panama. Arbuckle also drafted the six players who landed Brad Lidge and Joe Blanton in trades.
Ken Mandel is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.