As expected, in-house candidate Trent Baalke was named the 49ers general manager today, according to a league source familiar with the just-made decision.

Baalke has been considered the front runner ever since team president Jed York announced he would hire a GM last week in St. Louis. Baalke spent the past nine months acting as a GM, but with the title of vice president of player personnel.

He assumes the post vacated by Scot McCloughan for undisclosed reasons in March. Baalke’s primary challenger turned out to be former Raiders executive Michael Lombardi, who came with strong recommendations from Patriots coach Bill Belichick and Chiefs GM Scot Pioli, according to a source close to the search.

York decided to stick with someone he knew and was comfortable working with. Baalke has been in the organization for six years, rising from a western region scout to head of the personnel department.

Baalke’s first chore: Hire a head coach.

Stanford coach Jim Harbaugh remains the clear No. 1 choice, but the 49ers have already requested permission to interview minority candidates Hue Jackson, offensive coordinator of the Raiders, and Perry Fewell, defensive coordinator of the Giants.

Lombardi has prior work experience with Harbaugh from their time with the Raiders earlier this decade. However, one team source is convinced Harbaugh would be willing to work with Baalke — if he decides to work here at all.

More to come …