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Zhao, who stepped down as Binance chief executive in 2023, wrote on social media on Thursday that he was "deeply grateful for today's pardon and to President Trump for upholding America's commitment to fairness, innovation, and justice".
The pardon lifts restrictions that had stopped Zhao from running financial ventures, but it's not yet clear whether it changes his standing with US regulators or his ability to lead Binance directly.
In a statement Binance called the decision "incredible news".
The exchange, which is registered in the Cayman Islands, remains the world's most popular platform for buying and selling cryptocurrencies and other digital assets.
It did not respond to further questions about the conflict of interest claims.
Before the pardon, Zhao's companies had partnered with firms linked to Trump on new digital-currency projects including Dominari Holdings, where his sons sit on the board of advisers and which is based in Trump Tower.
The Wall Street Journal also previously reported representatives of the Trump family - which has its own crypto firm World Liberty Financial - had recently held talks with Binance.
The Trump administration previously halted a fraud case against crypto entrepreneur Justin Sun, after his investments in the Trump family's crypto firm, World Liberty Financial.
He has also pardoned founders of the crypto exchange BitMEX, who also faced charges related to money laundering, and Ross Ulbricht, founder of the Silk Road, the dark web marketplace known as a place for drug trade.
Palantir co-founder Joe Lonsdale wrote on social media that he loved Trump but the president had been "terribly advised" on pardons.
"It makes it look like massive fraud is happening around him in this area," he said.
Senator Elizabeth Warren, a Democrat, blasted the decision in a statement as a "kind of corruption".
Asked about the decision to pardon Zhao on Thursday, Trump appeared not to not know who he was.
