Both men pleaded not guilty to a series of charges in a 12-count indictment in a Washington DC court appearance.
The charges range from money laundering to acting as unregistered agents of Ukraine's former pro-Russian government.
According to a review of the charges by The Associated Press, Manafort potentially faces up to 80 years in prison while Gates could be hit with a 70-year sentence.
The extremely detailed FBI charges claim the two men “acted as unregistered agents of the Government of Ukraine” and its president Victor Yanukovych from 2006-2015.
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They were legally required to declare their work lobbying on behalf of a “foreign principal” such as a foreign government or political party, however they are alleged to have hidden it from the US government. They allegedly also funneled over $75 million (£57 million) through offshore bank accounts and did not pay any tax on their income from Ukraine.
It is claimed Mr Manafort personally laundered over $18 million (£14 million) through offshore accounts, which he used to fund a “lavish lifestyle” in the US, while Mr Gates funnelled $3 million into his own bank accounts.
The FBI charges say the two men “funnelled millions of dollars in payments into foreign nominee companies and bank accounts”, with offshore accounts in Cyprus, Saint Vincent and the Grenadines, the Seychelles, and even in the UK.
It also claims the businessmen gave “false and misleading statements” to the Department of Justice when they were asked about their work in 2016.
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The indictment gives details of 12 shell companies in Cyprus, two in the Grenadines, and one in the United Kingdom. There were also 23 holding companies in the US allegedly belonging to Mr Manafort.
Both Mr Manafort and Mr Gates hid the existence of these accounts, “falsely and repeatedly reporting to their tax preparers and to the United States that they had no foreign bank accounts”, the indictment says.
While not paying any tax on his earnings as a lobbyist for the Ukrainian government and President Yanukovych’s Party of Regions, it is alleged Mr Manafort “used his hidden overseas wealth to enjoy a lavish lifestyle in the United States”.
Payments detailed in the indictment show Mr Manafort purchased a Mercedes Benz, multiple Range Rovers, expensive clothes and antiques with money funnelled through the offshore accounts.
He also paid a landscape gardener $164,740 to work on his home in the Hamptons.
The news comes after another former Trump aide, George Papadopoulos, pleaded guilty to lying to the FBI earlier this month.