The cult rock band's frontman Aaron Freeman - also known as Gene Ween - confirmed the break-up in an interview with Rolling Stone.
He said: "It's time to move on. I'm retiring Gene Ween... It's been a long time, 25 years. It was a good run."
However, bandmate Mickey Melchiondo, aka Dean Ween, later appeared to be unaware of the split on their Facebook page. He said that the break-up was "news to me, all I can say for now I guess", before the post was removed.
Of the band's end, Freeman added: "For me it's a closed book. In life sometimes, in the universe, you have to close some doors to have others open. There's no, 'Goddamn that such and such!' For me, I'd like to think it's a door I can close finally."
Ween formed in Pennsylvania back in 1984, before releasing 11 studio albums between 1990 and 2007.
Their biggest hit was 1993's 'Push th' Little Daisies' from their 1992 LP Pure Guava.
Watch the video for 'Push th' Little Daisies' below: