The last known person seen with a California college student who vanished in 1996 was charged with her murder on Tuesday, authorities said.

Paul Flores, 44 — who was named last month as the “prime suspect” in the decades-old disappearance of Kristin Smart — was arrested around 7:30 a.m. in the Los Angeles area, according to the San Luis Obispo Sheriff’s Office.

His father, Reuben Flores, 80, was arrested as an accessory to murder at his home in Arroyo Grande — where investigators conducted a search warrant last month in the case.

Smart, a 19-year-old from Stockon, was last seen around 2 a.m. on May 25, 1996 on the campus of California Polytechnic State University in San Luis Obispo. She was declared dead in 2002, although her body has not been found.

Paul Flores, then also a 19-year-old freshman, had walked Smart home from an off-campus party that night, authorities said. She never made it back to her dorm.

“Throughout our investigation Paul Flores has remained a person of significant interest,” Sheriff Ian Parkinson said at a press conference on the campus Monday. “As the case progressed, he became a suspect and our prime suspect.”

Parkinson said additional evidence found in late 2016 confirmed that Flores was the suspect. 

In 2019, investigators spoke to witnesses who had previously not been interviewed — based on information uncovered in “Your Own Backyard,” a 2019 podcast about Smart’s disappearance.

Detectives conducted several other searches of Flores’ home, including in April 2020 when they found “evidence related to the murder” and in March where “more evidence was discovered,” Parkinson said.

“The sheriff’s office has been authorized to utilize cadaver dogs and ground-penetrating radar during the course of the search,” the department said last month. “This is an active and ongoing investigation.”

The sheriff said he couldn’t reveal what new evidence was discovered because the search warrants were sealed. That information will be revealed in court.

Defense attorney Robert Sanger confirmed to the Associated Press that Paul Flores was arrested in Smart’s case, but details of the charges he faces were not immediately available.

Flores, who had been considered a person of interest in the case prior to being named its top suspect last month, has been uncooperative with investigators.

Flores was arrested on a weapons charge last month after a search warrant was executed at his Los Angeles County home.

Investigators have not said what they found during the search of Ruben Flores’ home, the San Luis Obispo Tribune reported.

Paul Flores was being held without bail with an arraignment set for Thursday. His dad was being held on $250,000 bail.

A spokesman for Smart’s family said that news of the two arrests prompted “really emotional moments” from her relatives.

“A lot of prayers, astonishment, excitement, happiness, and of course sadness. Sadness, because this has gone on for 25 years,” family spokesman John Segale said. “The Smart family had not been able to bury their daughter. There was no closure.”

Investigators are still searching for Smart’s remains.

“We will find Kristin,” Parkinson vowed Monday.

With Post wires