Gowers leaves the FT after 22 years and just over four as editor. He was named editor in September 2001. Gowers' previous roles included Middle East editor, features editor, foreign editor, deputy editor and founding editor of Financial Times Deutschland.
A spokesman woman said that the decision for Gowers to depart cames after "strategic differences with Pearson".
The spokeswoman would not elaborate on who took the decision for Gowers to leave.
His departure follows a positive week for The Financial Times, which earlier this week said it expected to break even by the end of the year after a troubled first half of 2005.
Marjorie Scardino, chief executive of Pearson, said: "We're very grateful to Andrew for his distinguished 22-year career at the FT. As editor, he led the integration of print and online media, extended our international reach and steered the FT through the most difficult markets in its history."
New FT editor Barber, 50, joined the FT 20 years ago, having begun his career as a business journalist at The Scotsman and The Sunday Times. His roles at the FT have included Washington correspondent and US editor from 1986 to 1992, Brussels bureau chief from 1992 to 1998 when he became news editor. He spent a further two years as editor of the FT's European edition before in 2002 he moved to New York as the FT's US managing editor.
A nine-month trading update from Pearson revealed that FT Group sales were up 5% and advertising revenues for the FT were up 6%.
In July, it emerged that the FT lost around £3m for the first six months of the year.
The most recent set of ABCs showed a 5.96% rise from 413,882 in August to 438,538 in September. Circulation for the first nine months of the year is down 0.08% on the same period last year.
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