Mueller's latest move comes just a day after former US attorney Harry Litman said he thought the president's former campaign manager will be sent to jail by Friday.
Both were charged in a District of Columbia federal court with obstruction of justice and conspiracy to obstruct justice when they allegedly sought to make contact with two witnesses earlier this year.
Shortly after, Mueller's team said this week, Manafort and Kilimnik called and sent encrypted texts to two public relations individuals, attempting to persuade them to characterize the pro-Ukraine lobbying work they'd done together as limited to Europe.
The obstruction charges are related to a filing earlier this week in which Mueller's investigators alleged that Manafort and Kilimnik, also linked to Russia's intelligence service, attempted to tamper with the two un-named witnesses - going so far as to allegedly coach their testimony.
Kilimnik, according to court papers, wrote a message to the other executive two days later saying: "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 goal of the program was European Union".
According to Ukrainian journalists, kilimnik was in charge of the office of Manafort in Kiev since 2005 and 2015, is a citizen of the Russian Federation and Ukraine, and in the past was a military translator.
The expanded criminal allegations ratchet up the pressure Manafort faces to cut a deal with the special counsel's office as he awaits two criminal trials.
Authorities charge that the conduct of Manafort and Kilimnik amounts to witness tampering and have asked a judge to revise or revoke Manafort's bail package.
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The FBI has assessed that Kilimnik had ongoing ties to Russian intelligence, including during the 2016 presidential campaign when Manafort and Gates were in contact with him, prosecutors have said in court filings.
Paul Manafort leaves the E. Barrett Prettyman Federal Courthouse in Washington, D.C. on February 28, 2018. The individuals shared communications with prosecutors, the government said.
That day was the first time prosecutors also revealed they knew about Manafort's efforts to pay an influential group of European politicians, called the Hapsburg group, 2 million to help his Ukrainian lobbying clients.
The new charges will factor heavily into whether U.S. District Judge Amy Berman Jackson allows Manafort to remain on house arrest.
They said Manafort's "limited communications can not be fairly read, either factually or legally, to reflect an intent to corruptly influence a trial witness". Manafort deputy and co-defendant Rick Gates had pleaded guilty to lying to investigators and to a conspiracy charge. Gates is cooperating with prosecutors against Manafort.
The men continued to work together for a successor party to Yanukovych's after he fled Ukraine in February 2014 amid protests of his regime's corruption and pivot toward Moscow, eventually arriving in Russian Federation and effectively ending his presidency.
In Friday's indictment, Mueller accused Kilimnik of taking part in the covert lobbying scheme, and in trying to influence potential witnesses.
In addition, one of the officials said, Kilimnik's reported trips to the U.S.in May and August 2016 during Trump's campaign have "attracted attention" as to whether Manafort and Kilimnik tried to capitalize on Manafort's campaign role by offering Russian oligarch Oleg Deripaska private briefings.