Mr. Kilimnik was born in Ukraine when it was still a part of the Soviet Union, and he served briefly in the Russian Army as a linguist, later telling associates that he had a background with Russian intelligence. But this year, as scrutiny mounted of his work with Mr. Manafort in Ukraine, Mr. Kilimnik steadfastly denied any association with Russian intelligence. And an investigation by Ukrainian prosecutors into Mr. Kilimnik’s possible links to Russian spy agencies was closed late last year without charges.
Monday’s filing is notable because it marks the first official effort by Mr. Mueller’s team to connect Mr. Manafort to Russian intelligence. It appears to tie the case against Mr. Manafort more closely to the focus of the special counsel’s probe: connections between Russia and Mr. Trump and his associates, including whether they conspired to influence last year’s presidential election.
The United States intelligence community has concluded with “high confidence” that Russian intelligence tried to interfere in the election on behalf of Mr. Trump, and at the instruction of President Vladimir V. Putin of Russia.
Mr. Kilimnik has maintained residences in Moscow and Kiev, the capital of Ukraine, and has traveled regularly between them during about a decade of working for Mr. Manafort on behalf of various Russia-aligned oligarchs and political parties.
Mr. Manafort has told associates that he does not believe that Mr. Kilimnik has ties to Russian intelligence. And he told The New York Times in February that he had “never knowingly spoken to Russian intelligence officers, and I have never been involved with anything to do with the Russian government or the Putin administration or any other issues under investigation today.”
But he added, “It’s not like these people wear badges that say, ‘I’m a Russian intelligence officer.’”
Mr. Manafort and Mr. Kilimnik communicated regularly during the 2016 campaign, with Mr. Kilimnik traveling to the United States to meet at least twice. The pair exchanged cryptic emails last year in which they appeared to discuss how to use Mr. Manafort’s role on the Trump campaign to recoup unpaid bills from the Russian oligarch Oleg V. Deripaska.