Federer, who owns a record 17 Grand Slam titles, announced Saturday on his website that he will stop working with Annacone after 3 1/2 seasons together.
"After numerous conversations culminating at the end of our most recent training block, we felt like this was the best time and path for both of us," the posting continues.
The move comes only two days after Federer's latest surprising loss in a year filled with them: He was beaten 6-4, 6-7 (5), 6-3 in the third round of the Shanghai Masters by Gael Monfils, a former top-10 player now ranked 42nd and recently back from injury.
The defeat hurt the 32-year-old Federer's chances of qualifying for the season-ending ATP Tour Finals, a tournament that gathers the top eight singles players.
Federer used to be a lock for the field, year-in and year-out—he spent more weeks at No. 1 in the ATP rankings than any other man. But Federer was ranked only No. 7 last Monday and is no longer nearly the dominant presence he was for a decade.
The tournament in China was the first for Federer since his fourth-round exit at the U.S. Open, where he lost to 19th-seeded Tommy Robredo in straight sets on Sept. 3.
"Roger, when he was No. 1, (compared) to the Roger right now," Robredo said that day, "he's not maybe (playing) with the same confidence, no?"
Federer has struggled at times in 2013 with a bad back.
He lost in the semifinals at the Australian Open in January, the quarterfinals at the French Open in early June, and the second round of Wimbledon—against a player ranked 116th—in late June. That ended Federer's record run of reaching at least the quarterfinals at 36 consecutive major tournaments.
The loss to Robredo gave Federer a new, unwanted streak that he will carry into the 2014 Australian Open: two consecutive losses before the quarterfinals at majors.
His last Grand Slam championship came in 2012 at Wimbledon, which he won for the record-tying seventh time. That allowed Federer to return to No. 1 in the rankings, ended a 2 1/2-year major title drought—and marked the lone Grand Slam trophy Federer and Annacone won as a pair.
In Saturday's announcement, Federer refers to a three-year plan he and Annacone, who previously worked with Pete Sampras, established in order to earn a Grand Slam title and a return to No. 1.
"Along with many other goals and great memories," the posting says, "these 2 main goals were achieved."
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