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A DNA sample from accused Gilgo Beach serial killer Rex Heuermann linked him to at least one of the women he is accused of killing 13 years ago — and to a pizza crust that helped crack the cold case, prosecutors said in court Wednesday.

Heuermann, 59, submitted the court-ordered swab last month, with Suffolk County prosecutors now saying that the sample matched DNA from a pizza crust found outside his Midtown Manhattan office in July — which matched a hair found on the body of Gilgo Beach victim Megan Waterman in 2010.

The DNA on the discarded crust had previously been tied to Heuermann’s estranged wife, Asa Ellerup, not him directly — until now, according to prosecutors.

“The surveillance team had observed the pizza box and were confident that that was the DNA, that the DNA profile would be consistent with the defendant because he left that material inside the box,” Suffolk County District Attorney Ray Tierney told reporters after the hearing. “And so the buccal swab just erases all doubt.”

The hulking architect — who wore tan pants, a white shirt and a jacket and sported a new haircut with a comb-over as he appeared in court — is charged with murder in the deaths of three women who were found dumped along Gilgo Beach in December 2010: Waterman, 22, Melissa Barthelemy, 24, Amber Lynn Costello, 27.

He is also the prime suspect in the death of a fourth woman, 25-year-old Maureen Brainard-Barnes — with the victims, all former sex workers, known collectively as the “Gilgo Four.”

Heuermann only spoke once during the brief proceedings, telling Suffolk County Supreme Court Justice Timothy Mazzei that he had been able to review evidence submitted by prosecutors “2 or 3 hours” at a time from behind bars.

Outside the courtroom, Heuermann’s lawyer disputed the importance of the alleged match from his client’s DNA swab.

“There is nobody on the face of the earth that is credible is going to say that hair is my client’s hair,” defense attorney Michael Brown said. 

“It’s impossible under science standards,” he said. “What they can do is say he could potentially be a donor for that hair, but so could thousands and thousands of other people just in our area, so take that for what it’s worth.”

Brown also replied to earlier comments from the county sheriff that Heuermann had shown no emotion after his arrest – saying that he had advised his client, “Don’t let anything upset you.”

“Just be stoic,” Brown said he told Heuermann. “And that’s what he’s done.”

More than 10 sets of human remains were found along Ocean Parkway on Long Island’s South Shore in 2010 and 2011, with their deaths a mystery for 13 years.

In January 2022, newly appointed Suffolk County Police Commissioner Rodney Harrison, a decorated former NYPD chief, vowed to reopen the Gilgo investigation — and identified Heuermann as a suspect within three months.

Police used cell phone records, former witness accounts and the DNA link from the pizza, which was found at Heuehermann’s Manhattan office and hair found on up to two of the Gilgo Beach victims to help make their case.

One witness, David Schaller, who described himself as Costello’s roommate, gave police a description fitting Heuermann and even described the architect’s distinctive Chevy Avalanche shortly after she went missing on Sept. 2, 2010, but police did not follow up on the tip for more than a decade.

The hulking architect was taken into custody outside his office on July 13, with investigators then turning their attention to the Massapequa Park home where he grew up and still lived with his family.

Brown said Wednesday that cops had surveillance cameras pointed at the house for months before they busted Heuermann.

“What the DA’s office did is they set, and the police department I should say, they had pole cameras focused on my client’s house for a year and a half prior up until the arrest,” he told reporters.

Heuermann bought the home from his mother, Dolores, in 1994 before her death, and was living there with his wife, Asa Ellerup, her developmentally disabled son, Christopher Sheridan, and the couple’s daughter, Veronica Heuermann, who worked as a receptionist in her dad’s office.

Ellerup and her kids were kicked out of the home while investigators combed through the house looking for body parts or other evidence for 12 days, even digging up the backyard.

In her first interview since her husband’s arrest, Ellerup told The Post on July 31 that cops left the house in complete shambles — and the family so traumatized that they had trouble sleeping when they returned.

“I woke up in the middle of the night, shivering,” she said. “My children cry themselves to sleep. I mean, they’re not children. They’re grown adults but they’re my children, and my son has developmental disabilities and he cried himself to sleep.” 

Ellerup, who married Heuermann in 1996, filed for divorce after his arrest.

On Wednesday, her lawyer reiterated that his distraught client has continued to speak with Heuermann by telephone but has not been to see him at the Suffolk County Jail.

“They’ve spoken on the phone, yes. She has not visited him,” attorney Robert Macedonia said. “She’s keeping an open mind at this point.”

According to authorities, Heuermann would frequently solicit escorts on Craigslist and other online sites, while cops found videos with pornographic and violent sex content on his computer.

He pleaded not guilty at his arraignment on the murder charges in July and is being held without bail at the Suffolk County Jail.

The discovery of the Gilgo Beach bodies stemmed from the search for 23-year-old Shannan Gilbert, a New Jersey escort who vanished on Long Island on May 1, 2010.

Investigators searching for Gilbert stumbled upon the first of the Gilgo Beach bodies in December 2010, and over the following year would uncover the other bodies — including Gilbert’s, which was found on Dec. 13, 2011, in a marshy area in Oak Beach, about 7 miles from the Gilgo Four.

Gilbert’s death and that of the other victims found along Ocean Parkway remain unsolved.

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