By Keach Hagey And Joe Flint 

Jon Stewart will retire as the host of Comedy Central's "The Daily Show, " the cable network said, after a nearly 16-year run that helped reshape late-night television.

In a statement, Comedy Central President Michele Ganeless said Mr. Stewart will remain at the helm of the show until later this year.

"Through his unique voice and vision, 'The Daily Show' has become a cultural touchstone for millions of fans and an unparalleled platform for political comedy that will endure for years to come," she said. "He is a comic genius, generous with his time and talent, and will always be a part of the Comedy Central family."

Mr. Stewart's contract is set to expire in September, and negotiations on the exact timing of his departure from the show are still under way, according to a person familiar with the matter.

Mr. Stewart's departure will follow that of Comedy Central's other high-profile late-night comic, Stephen Colbert. Mr. Colbert ended his program, "The Colbert Report," late last year and will begin hosting a late-night talk show on CBS in 2015.

The loss of top talent at Comedy Central poses challenges for the channel's parent, Viacom Inc., which is already trying to rebound from ratings declines at several of its major networks.

After Mr. Colbert's departure, the network created a show for Larry Wilmore, who was known as the "senior black correspondent" on "The Daily Show." Mr. Wilmore's program, "The Nightly Show," premiered last month.

Mr. Stewart has become a major voice in American culture. He has lampooned political figures and skewered the media with trademark montages taken from the day's news. And he has used his platform to conduct serious and, at times, probing interviews with major news makers.

"The Daily Show" also proved to be an excellent springboard. Several members of Mr. Stewart's team became stars in their own right, including Steve Carell, Mr. Colbert and John Oliver. Mr. Oliver now hosts a show on Time Warner Inc.'s HBO.

"The Daily Show" has always drawn a relatively small but influential audience in the world of late night, averaging 1.7 million total viewers for this quarter, according to Nielsen. But the audience has always been highly attractive to advertisers for its ability to consistently pull in the elusive young male audience in the 18-34 demographic.

Mr. Stewart took over the Daily Show in 1996 from Craig Kilborn who left for a late-night show on CBS.

Write to Keach Hagey at keach.hagey@wsj.com

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