Former Newcastle and Manchester City star Barton has been in charge of the League One side since February 2021.
Rovers are 16th in the table and have won one of their last five games.
A statement from the club read: "Bristol Rovers Football Club can confirm that today the club has relieved First Team Manager Joey Barton of his duties.
"Everyone at the club would like to thank Joey for all his efforts and wish him well in the future.
"In the interim, Andy Mangan will lead the team supported by Glenn Whelan, Danny Ventre and Anssi Jaakkola who will remain in post."
Barton's last game in charge came in Tuesday's game at home to Stevenage as his side salvaged a late 1-1 draw.
He will be fondly remembered for orchestrating Rovers' incredible final-day promotion to League One in 2022.
Rovers went into the final round of fixtures needed a five-goal swing over Northampton.
An incredible 7-0 victory over Scunthorpe moved his side into the final automatic promotion place, causing heartbreak for the Cobblers.
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Barton signed a new three-year deal in July 2022 before leading The Pirates to a 17th-placed finish last season.
But failure to kick on this term has ultimately sealed his fate as Rovers begin their search for his successor.