The roommate of one of the two University of South Florida graduate students who mysteriously disappeared this week has been charged with their murders.

Hisham Saleh Abugharbeih — who was arrested after cops found 27-year-old Zamil Limon’s body Friday — is now facing two counts of first-degree premeditated murder with a weapon, the Hillsborough County Sheriff’s Office announced.

Abugharbeih had originally been facing failure to report a death and unlawfully moving a body, as well as battery and false imprisonment.

The details of what officials called a “disturbing” case were still unclear, but police said they had gathered enough evidence to prove Abugharbeih had killed Limon and his girlfriend, Nahida Bristy, 27, who is assumed dead.

Dive teams returned to Old Tampa Bay near the Howard Frankland Bridge on Friday to continue the search for Bristy’s body after Limon’s remains were found nearby.

Limon’s cause of death was under investigation.

Abugharbeih was arrested after barricading himself inside a Tampa home Friday, officials said.

SWAT teams armed with assault rifles descended on Limon’s Lake Forest neighborhood —  just over a mile from USF’s Tampa campus, where Limon and Bristy were students.

The raid was tied to the alarming disappearance of the couple soon after officials, without elaborating, had declared they were deemed “endangered.”

The situation was “resolved” about two hours later, the sheriff’s office said, with Abugharbeih taken into custody.

“This is a deeply disturbing case that has shaken our community and impacted many who were hoping for a safe resolution,” said Sheriff Chad Chronister. 

“While the discovery of Zamil Limon’s remains is heartbreaking, I want the public to know that our detectives worked and are working tirelessly and relentlessly to uncover the truth. We will continue to follow every fact, pursue every lead, and use every tool available to hold those responsible fully accountable.”

Limon and Bristy, a couple from Bangladesh, were last seen in the area on April 16.

They were reported missing by a friend who said they were unable to get in touch with the pair. Both of their phones had been turned off, investigators said.

Limon was a doctoral student pursuing a degree in geography, environmental science and policy, while Bristy was studying chemical engineering.

The students had recently discussed getting married.