SANTA CLARA — Paraag Marathe’s stint as the 49ers president is nearing an end after almost two years, though he’s remaining with the franchise to handle other interests, according to sources Thursday night.

Al Guido has taken on more responsibilities within the organization over the past year while Marathe’s duties have shifted. Guido assumed Marathe’s former role of chief operating officer in January 2014.

Marathe’s reassignment also was reported by Comcast SportsNet Bay Area, which noted that Marathe would remain the 49ers’ lead salary-cap administrator and top contract negotiator.

Team CEO Jed York, in a text message to this newspaper earlier Thursday night, said Marathe was “still the president” and “going to be part of the team and businesses that my family runs for a long time.”

Marathe will retain his title as president through Super Bowl 50, which will be held Feb. 7 at Levi’s Stadium, CSN Bay Area reported.

News of the front office’s restructuring comes with the 49ers (3-8) mired in last place in the NFC West and assured their second straight non-winning season.

Marathe has long worked closely with general manager Trent Baalke and often sat next to him at games in the press box. Baalke is in his sixth season overseeing player personnel, and his contract is set to expire after the 2016 season.

Marathe, 38, made a remarkable rise through the 49ers front office since joining the franchise in 2001, eventually claiming the role of team president on Jan. 21, 2014, when he replaced minority owner Gideon Yu in that role.

Beside his football duties, Marathe is helping Sacramento’s push to land a Major League Soccer team and build a downtown stadium. He’s also a key figure in VenueNext, a startup that creates in-stadium apps such as the one for Levi’s Stadium.

Marathe’s acumen as the chief negotiator on player contracts and salary-cap management had solidified his place in the 49ers’ hierarchy. Meanwhile, Marathe also developed contentious and distrustful relationships with some players and agents, multiple league sources said.

An NFL source told this newspaper that Marathe was being deposed as president in part because he is believed to be the source of many recent leaks to national reporters, most notably the reports discrediting quarterback Colin Kaepernick.

Marathe has been an avid proponent of statistical analytics throughout his 15 years with the franchise, an area that’s been welcomed by some and scorned by others.

Before his appointment as president, Marathe was the chief operating officer for three years, supervising such aspects as business operations, production, marketing, ticketing and suites, and stadium operations. He became the 49ers’ chief contract negotiator in 2004.

Marathe was named this year to Sports Business Journal’s Forty Under 40 list. He’s been a lecturer at Stanford and a guest speaker at the MIT SLOAN Sports Analytic Conference.