"Manafort and Kilimnik repeatedly contacted Persons D1 and D2 in an effort to secure materially false testimony", prosecutors alleged in court papers.
Mueller's new indictment comes as Trump and his allies, including his personal lawyer Rudy Giuliani, increase their public attacks on Mueller's investigation and pressure the special counsel to bring his work to a close.
Kilimnik, widely believed to be a former agent for the Kremlin's top intelligence agency, GRU, has been working for Manafort in various capacities since they lobbied for Russia-backed ex-Ukrainian President Viktor Yanukovych in the early 2000s.
A spokesman for Mueller issued a statement on Friday saying: "A federal grand jury in the District of Columbia has returned a third superseding indictment today against Paul J Manafort Jr, 69, of Alexandria, Virginia, which adds Konstantin Kilimnik, 48, of Moscow, Russia, as a defendant and charges both defendants with conspiracy to obstruct justice and obstruction of justice".
The witnesses placed op-eds from the politicians and arranged meetings for them in the United States and around the world, according to court papers. The spokesman, Jason Maloni, said Friday that Manafort and his attorneys were reviewing the new charges.
In the piece, writer Christopher Strohm argues that the charges against Kilimnik represent a breakthrough in the case because it "links senior officials on President Donald Trump's presidential campaign to Russian intelligence in a criminal matter". He faces a second trial in Washington in September.
Manafort messaged and called one of the witnesses shortly after he and business partner Rick Gates were indicted a year ago on a slew of charges related to their Ukrainian political activities, according to court papers.
Kilimnik, who isn't in the US and didn't immediately respond to a request for comment, has denied any links to Russian intelligence. The previously pending charges against Manafort of course had nothing to do with the synthetic collusion hyseteria over the 2016 election. The individuals shared communications with prosecutors, the government said.
Manafort faces two other indictments on a laundry list of charges, including conspiracy against the USA, money laundering and tax fraud. Manafort has longstanding ties to a pro-Russian political party in Ukraine and a Russian oligarch close to the Kremlin.
Mueller has accused Manafort of attempting to call, text and send encrypted messages in February to two people from "The Hapsburg Group", a political discussion group he allegedly worked with to promote the interests of Ukraine, in an effort to influence their testimony or hide evidence in the case. Kilimnik has denied such ties and characterized himself as "a random casualty because of my proximity to" Manafort.
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".
Kilimnik remained in contact with Manafort during the period when Manafort was serving as chairman of Trump's presidential campaign in 2016.
Manafort joined the Trump campaign in March 2016, was promoted to campaign manager in May 2016, and stayed until August 2016, having played a major role during the Republican National Convention.
In Friday's indictment, Mueller accused Kilimnik of taking part in the covert lobbying scheme, and in trying to influence potential witnesses. Kilimnik later took on more responsibilities, serving as Manafort's liaison to Oleg Deripaska, a Russian billionaire who paid Manafort to advise him on investments.