US special counsel Robert Mueller brought the charges as part of a wide-ranging investigation into Russian interference in the 2016 election, possible obstruction of justice, and alleged financial crimes by Manafort and others.
Trump has denied that his campaign colluded with Russia.
Manafort has also pleaded not guilty to separate charges including conspiracy to launder money and conspiracy against the United States. His trial on those charges is due to begin on 17 September.
Manafort was Trump’s campaign manager for five months in 2016. He was originally indicted last year with Gates, Trump’s former deputy campaign manager.
Gates agreed to cooperate with Mueller as part of a plea deal to charges that he lied to investigators and conspired against the United States.
Gates’ move was seen as adding to pressure on Manafort to cut a deal himself but he said in a statement after Gates’ plea deal that he maintained his innocence.
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