Manafort has voluntarily given documents to congressional committees investigating his role in allegations that the Trump campaign colluded with Russian Federation during the 2016 presidential election.
Manafort cooperated with authorities, spokesman Jason Maloni said.
The Associated Press has learned the warrant for the search July 26 at Manafort's home in Alexandria, Va., sought information including tax documents and banking records.
United States media have also quoted sources close to the inquiry as saying Mr Mueller is investigating whether the president could have obstructed justice when he fired FBI chief James Comey, who was leading the previous investigation into Russian interference.
As pollster Matt McDermott noted on Twitter, President Trump vented his anger against the acting Federal Bureau of Investigation director only hours after the raid.
The Washington Post first reported news of the raid Wednesday morning. Agents presented Manafort with a wide-ranging search warrant as they raided his residence and collected various documents and other materials.
Manafort has been cooperating with the congressional committees in their Russian Federation probes, meeting with staff members behind closed doors and turning over documents.
This is also the day after Manafort had met with the Senate Intelligence Committee and voluntarily provided them with documents they had requested.
A spokesman for Mueller would neither comment on nor confirm the raid.
Manafort is only one focus of the Russian Federation probe as Mueller has a team of 16 attorneys working on the investigation according to Politico.
Mr Manafort received $17.1m (€14.5m) for his work with a Ukrainian political party, according to a foreign agent registration document he filed with the United States government in June. That may explain why we haven't seen any angry presidential tweets directed at Wray, or perhaps more damning, statements of "support" of the new director. Trump Jr. had apparently been under the impression the lawyer had damaging information on his dad's opponent Hillary Clinton, yet all they ended up talking about was adoption.
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