Two prosecutors heading the Manhattan District Attorney's Office's probe into the Trump Organization called it quits on Wednesday — throwing the case into question.

The DA's office confirmed the resignations of Mark Pomerantz and Carey Dunne.

A source told The Post that the prosecutors jointly stepped down, stressing that the coordinated nature of the departures was a sign of intense frustration with the direction of the case.

"We are grateful for their service," DA spokeswoman Danielle Filson said in a statement. She declined to comment further, saying the probe is ongoing.

The investigation into former President Donald Trump was launched in 2018 under then-DA Cyrus Vance, who charged the Trump Organization and its longtime chief financial officer Allen Weisselberg with tax fraud last June.

Vance convened another grand jury before new District Attorney Alvin Bragg took over in January.

Dunne, who joined the office in 1984 and served as Vance's general counsel, had overseen the investigation from the outset, successfully arguing before the US Supreme Court for Trump's tax records. Pomerantz, a former federal prosecutor in Manhattan and criminal defense attorney, was brought on by Vance last year to join the probe. Neither immediately returned messages.

The New York Times, which first reported the move, said it came after Bragg suggested to the attorneys that he had doubts about moving forward. Prosecutors had been questioning witnesses before the grand jury until about a month ago, essentially stopping the investigation, according to the Times.

Without Pomerantz and Dunne there to steer the probe, its future is uncertain.

Criminal defense attorney Ron Fischetti, who represents Trump and his company, told The Post he saw the resignations coming and was "happy" with the development, while maintaining his clients' innocence.

He said there was "no investigation" without Pomerantz and Dunne, adding that the resignations were a sign that Bragg could soon close the case.

The DA's Office didn't comment on whether the case was still moving forward.

Bragg hasn't said much about the investigation publicly since taking office. During a media availability in late January, he said he was still "getting up to speed" and "following the facts," adding that he was constrained from saying more.

The criminal probe coincides with New York Attorney General Letitia James' investigation into the Trump Organization's business dealings.

A Manhattan judge ruled last week that Trump and two of his children, Ivanka and Donald Jr., must testify in that investigation.

Trump's camp had argued against the subpoenas, claiming the AG's office would use the depositions to aid the probe by the DA's office, rather than calling the family members before a grand jury.

Two Manhattan prosecutors leading Trump Organization probe resign