Although Kilimnik denies it, Mueller's first indictment alleges that he had ties to Russian intelligence as late as 2016.
For Manafort though, the charges come at a perilous time, just hours before his lawyers were due to file legal briefs explaining why he should be allowed to remain free on bond pending his trial scheduled for next month in Alexandria, Virginia.
Manafort's trial is set for September 17.
They said Kilimnik may have reported to Russian intelligence officers in Moscow or Kiev or both on his work at the International Republican Institute office in Moscow where he was employed for a decade to 2005 and later on his work for Manafort in Ukraine.
The White House did not immediately comment on Friday's new charges, but some of Trump's allies quickly picked up a familiar argument.
Manafort has responded to the allegations that he tampered with witness evidence.
In Friday's indictment, Mueller accused Kilimnik of taking part in the covert lobbying scheme and of trying to influence potential witnesses.
"What you really care about is what information Mr. Manafort could give you that would reflect on Mr. Trump or lead to his prosecution or impeachment".
In court papers, the Federal Bureau of Investigation is alleging that at least one witness in the Manafort case was contacted by the former Trump aide and coached on what he should say about his lobbying practices.
'We should talk. I have made clear that they worked in Europe, ' Manafort wrote Person D in an encrypted message.
"Basically P wants to give him a quick summary that he says to everybody (which is true) that our friends never lobbied in the United States, and the objective of the program was EU", Kilimnik wrote.
Special Counsel Mueller files new charges against former Trump campaign manager Paul Manafort in Russian Federation probe; attorney Troy Slaten joins "your World" to discuss.
Manafort is now under house arrest.
In addition to the FARA charge, Manafort stands accused of tax fraud, bank fraud, and conspiracy against the United States.
Over in the District of Columbia, Judge Amy Berman Jackson will hold a hearing in Manafort's case on June 15, when she will rule on the prosecutors' motion to revoke Manafort's bail, and jail him until the start of the trial.
It was the third time Mueller had added to charges against Manafort since he was indicted in October. One project was to assemble a team of European political leaders who could advocate for Ukraine's then-President Viktor Yanukovych - apparently independently. The politicians lobbied members of Congress and executive branch officials on Ukraine in coordination with Manafort and his longtime deputy and former co-defendant Rick Gates, according to prosecutors. Gates has already pleaded guilty and is cooperating with Mueller's investigation.
In previous court filings he was referred to only as "Person A" and described as having links to Russian intelligence. Kilimnik has denied such ties.
Emails show that during the middle of the campaign, Manafort told Kilimnik he was willing to provide "private briefings" about Trump's presidential run to a billionaire close to Russian President Vladimir Putin.