Robert Mueller indicted Mr Trump's former campaign chairman Paul Manafort and business associate Rick Gates on multiple counts of tax and bank fraud.
Both were charged in October with conspiracy to launder money.
But there are no criminal allegations of collusion with Russia, the Justice Department investigation's main thrust.
A spokesman for Mr Manafort said he was innocent of the latest charges. Mr Gates lawyer is yet to respond to requests for comment, Reuters reports.
Mr Manafort resigned as chairman of the Trump campaign in August 2016 after being accused over his dealings with pro-Russian politicians in Ukraine.
The seasoned political operative has worked on several Republican presidential campaigns, beginning with Gerald Ford's in 1976.
What are the new charges?
Thursday's 32-count indictment alleges that Mr Manafort and Mr Gates conspired to hide more than $30m (£22m) in Mr Manafort's personal income from tax officials.
It also claims that Mr Gates concealed more than $3m of his own income.
The money "flowed through" a $75m offshore account controlled by them, according to the indictment filed by a federal grand jury in Alexandria, Virginia.
It is also alleged the two defendants filed tax returns to the US authorities from 2010-14 that they knew to be factually incorrect.
Media captionManafort's indictment: Where did all the money go?
Mr Gates is accused of using his share of the cash to pay for "personal expenses, including his mortgage, children's tuition" and re-decorating his Virginia home.
Earlier on Thursday a court denied Mr Manafort's request to modify the terms of his house arrest.
The judge ruled that Mr Manafort's pledge to use his properties in Virginia and New York as bail collateral was "unsatisfactory".
The special counsel had opposed the bail application.
Mr Mueller's team argued the Manafort properties were related to "additional criminal conduct" and could be confiscated in the event of foreclosure.
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How many people has Mueller charged?
Nineteen people, including four former Trump advisers, have been indicted by the special counsel.
But as President Trump has repeatedly pointed out, the ongoing inquiry has filed no charge that any of his associates colluded with an alleged Kremlin plot to influence the result of the 2016 presidential election.
Mr Manafort and Mr Gates pleaded not guilty last October to 12 counts including money laundering and conspiracy against the US, relating to the pair's Ukrainian business dealings.
Michael Flynn, the former US national security adviser, pleaded guilty to lying to the FBI over meetings he had with the Russian Ambassador, Sergei Kislyak.
George Papadopoulos, a former Trump campaign adviser, admitted lying to the FBI about his contacts with Russians.
Last week, 13 Russians were charged with tampering in the 2016 US election and a California man, Richard Pinedo, admitted an identity theft charge.
This week a London-based lawyer, Alex van der Zwaan, pleaded guilty in court to making false statements when questioned about his work for Ukraine's Ministry of Justice.
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