The new charges against both men - known as a superseding indictment - alleges that they sought to tamper with witnesses ahead of Mr Manafort's trial next month.
Kilimnik has always been a close business colleague of Manafort's that prosecutors have said in previous filings has ties to Russian intelligence.
'They haven't been convicted of anything.
"T$3 he tactic that Mueller is using-telling Manafort that he will be charged-is generally used when prosecutors are trying to get a defendant to "flip.' This strongly suggests what we've long expected-that Mueller is trying to 'flip" Manafort", former federal prosecutor Renato Mariotti said at the time.
In the latest charges, prosecutors say the contacts with the witnesses via phone and encrypted messaging applications first occurred in February, shortly after Manafort's co-defendant, Rick Gates, pleaded guilty and agreed to cooperate with prosecutors.
The White House did not immediately comment on Friday's new charges, but some of Trump's allies quickly picked up a familiar argument.
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The fresh counts could make it harder for Manafort to avoid jail before he goes on trial for alleged financial crimes that largely predate his time on the Trump campaign. The work is the basis for the criminal case in Washington where Manafort faces charges of acting as an unregistered foreign agent, money-laundering conspiracy and false statements.
Is former Trump campaign chairman Paul Manafort's problem really that he has no dirt? Manafort had been close to getting court approval for a $10 million bail deal that would permit him to remain on electronic monitoring at home. He is being charged with obstruction of justice and conspiracy to obstruct justice.
Prosecutors complained to a federal judge earlier this week that Manafort - and, apparently, Kilimnik - had been contacting people who knew about that work to ask them to tell jurors that the Ukraine lobbying had only taken place inside Europe.
Yet Manafort and the public relations people had brought the Hapsburg group to the USA to speak with members of Congress about the interests of Viktor Yanukovych, a former Ukrainian president who had jailed a political rival, while posing as independent voices, prosecutors said earlier this week.
Perhaps more important is that an alleged line from the Russian government to the Trump campaign could be getting clearer.
The move in court came just hours after Trump said it was "too early" to consider pardons for Manafort or longtime Trump lawyer Michael Cohen.