Mueller issued a subpoena to Germany's largest lender several weeks ago, forcing the bank to submit documents on its relationship with Trump and his family, according to a person briefed on the matter, who asked not to be identified because the action has not been announced.
In June, President Trump disclosed that he owes the bank roughly $130 million.
Deutsche Bank, which has loaned the Trump Organization millions of dollars for real estate investments, refused to share Trump's financial information with U.S. House Democrats in June. Trump has denied any wrongdoing.
Mueller is investigating alleged Russian attempts to influence the 2016 US presidential election and potential collusion by Trump aides.
The bank holds a $170 million loan for his hotel in Washington and also has two mortgages on his Trump National Doral Miami resort and one loan on his tower in Chicago, Bloomberg reported.
German business paper Handelsblatt first reported the supoena, confirmed by Reuters through an anonymous source close to the matter.
The White House has not yet commented on Mueller's subpoena of Deutsche Bank.
This comes after Trump's former national security advisor Michael Flynn pleaded guilty to lying to the Federal Bureau of Investigation about his conversations with the Russian ambassador in January.
His plea deal came after Mueller revealed charges against former Trump campaign officials Paul Manafort and Richard Gates.
Trump has done billions of dollars' worth of business with Deutsche Bank in the past 20 years; he has previously said that he would consider Mueller looking into his finances beyond any connection to the Russian Federation investigation "a violation".
Russian Federation has denied meddling in the election and Trump has said there was no collusion.
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