Bolton's lawyer did not immediately respond to a request for comment. His lawyer had previously denied that Bolton engaged in wrongdoing.
Thursday's indictment, according to court records, comes after court documents made public in September revealed Bolton was under federal investigation for potential mishandling of classified information.
Trump, who campaigned for the presidency on a vow of retribution after facing a slew of legal woes once his first term in the White House ended in 2021, has dispensed with decades-long norms designed to insulate federal law enforcement from political pressures.
In recent months, he has actively pushed Attorney-General Pam Bondi's Justice Department to bring charges against his perceived adversaries, even driving out a prosecutor he deemed to be moving too slowly in doing so.
Bolton served as US ambassador to the United Nations as well as White House national security adviser during Trump's first term before emerging as one of the president's most vocal critics. He described Trump as unfit to be president in a memoir he released in 2024.
Asked by reporters at the White House about the Bolton indictment on Thursday, Trump said: "He's a bad guy."
The charges against Bolton come shortly after the Justice Department indicted former FBI director James Comey, who investigated Trump's 2016 presidential campaign, and New York Attorney-General Letitia James, who previously brought a civil fraud case against Trump and his family real estate company.
Comey, whom Trump fired in 2017, is facing charges of making false statements to Congress and obstruction of Congress. He has pleaded not guilty.
James is facing charges of bank fraud and making false statements to a financial institution. She has denied wrongdoing and is slated to appear in federal court later this month.
Senior leaders at the US Justice Department had been pushing for swift charges against Bolton, despite initial concern from some line prosecutors in Maryland, as well as Lawyers in the National Security Division who felt more investigation was needed and feared the case was being rushed, two people familiar with the matter previously told Reuters.
Prosecutors more recently concluded they were comfortable proceeding after taking more time to review the evidence and worked over the weekend to prepare the case, one of those sources added.
FBI agents conducted a search of Bolton's home and office in August, seeking evidence of possible violations of the Espionage Act, which makes it a crime to remove, retain or transmit national defence records, according to partially unsealed search warrants filed in federal court.
In his Maryland home, agents seized two mobile phones, documents in folders labelled "Trump I-IV" and a binder labelled "statements and reflections to Allied Strikes," according to court documents.
They also found records labelled "confidential," including documents that referenced weapons of mass destruction, the US mission to the UN, and other materials related to the US government's strategic communications inside his office in Washington DC., according to court records.
Court records also show that a foreign entity hacked Bolton's email account, though details of the hack are redacted. Bolton's lawyer has previously said that the records the FBI seized were ordinary documents for a former government official to possess.
Trump himself was previously indicted on Espionage Act violations for allegedly transporting classified records to his Florida home after departing the White House in 2021 and refusing repeated requests by the government to return them. Trump had pleaded not guilty and that case was dropped after he won reelection in November 2024.
The case against Bolton is being led by the US Attorney's office in Maryland. That office is separately investigating Trump's long-time critic Democratic US Senator Adam Schiff of California for possible mortgage fraud. Schiff has denied wrongdoing, and has not been charged with a crime.
