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Trump in a Fox News interview that aired Friday was asked whether he thinks Mueller should recuse himself from the Russia probe he is leading.
"Well, he is very, very good friends with Comey, which is very bothersome," Trump said. "We're going to have to see."
Trump fired Comey in May, shortly after which Mueller was appointed by Deputy Attorney General Rod Rosenstein to lead the FBI investigation of Russia's interference in the 2016 U.S. election and possible ties to Trump associates.
Trump asserted in the interview, "There's been no collusion, no obstruction and virtually everybody agrees to that."
The president also claimed that Mueller's team of lawyers are "all Hillary Clinton supporters."
Comey succeeded Mueller, who was FBI director from 2001 to 2013 under both Republican and Democratic presidents and has been a registered Republican through most of his career.
The attorneys hired onto Mueller's special counsel team were brought on using the same standards that the Department of Justice uses to hire career attorneys.
Under those standards, as described in a 2008 Justice Department Inspector General report, federal law and department policy prohibit assessing potential employees based on their political or ideological affiliations.
ABC News' Jack Date contributed to this report.