Protesters in the Philippines hang a rainbow banner from a foot bridge near the U.S. Embassy on Dec. 1 to demand justice for the Oct. 11 killing of Jennifer Laude, a transgender Filipina, at a former U.S. naval base northwest of Manila. (Bullit Marquez/Associated Press)

Prosecutors in the Philippines have formally charged a U.S. Marine with the October murder of a transgender woman.

Pfc. Joseph Scott Pemberton is accused of strangling and drowning Jennifer Laude in a toilet bowl, a case that Filipino advocates have called a “hate crime.”

Pemberton, 19, was among 3,500 U.S. troops in the country to participate in joint military exercises. But the murder case has raised new tensions that now threaten the longtime relationship between the United States and the Philippines, a former colony.

Prosecutors said they have “probable cause” to believe that Pemberton is responsible for Laude’s death.

“It’s murder,” prosecutor Emily de los Santos said, according to the Associated Press. “It was aggravated by treachery, abuse of superior strength and cruelty.”

According to the Philippine National Police, Pemberton allegedly met Laude and another transgender woman named Barbie at a disco bar while on shore leave in Olongapo City.

The three checked into a motel, but later that night, Laude told the other woman that they should leave before Pemberton could discover that they were transgender.

Laude was found next to a toilet by the motel clerk, dead by apparent drowning. Pemberton was identified by the motel clerk and by Barbie in a photo lineup. He was held on a U.S. assault ship docked off the Philippine coast. But after anti-American protests, he was moved to a Philippine detention camp on land but remained in U.S. custody, according to the AP.

Pemberton is a native of Bristol, Mass., who enlisted in the Marine Corps last year, according to a statement from Col. Brad Bartelt, spokesman for the Marine Corps Forces Pacific, based in Hawaii. Pemberton, an anti-tank missileman, is stationed at Camp Lejeune in North Carolina and is a member of the 2nd Battalion, 9th Marines. According to Bartlelt’s statement, Pemberton was promoted to his current rank on Oct. 1, just days before Laude’s death.

In evidence submitted in court by prosecutors, one of the three Marines who was with Pemberton that night said that the suspect allegedly confessed to attacking the woman he was with, according to the Associated Press.

Marine Lance Corporal Jairn Michael Rose said that later that night when they returned to the ship, Pemberton confided in him that after the woman undressed and he discovered that she was transgender, he choked her with his arm until she stopped moving. He allegedly then dragged her into the bathroom.

“I think I killed a he/she,” Pemberton was quoted as having told Rose, according to the AP.

Suspects charged with murder in the Philippines are not eligible for bail. And according to de los Santos, Pemberton, who has not been seen publicly since being charged, would have to appear in court for an arraignment.

According to Reuters, an arrest warrant is expected to be issued within the next week. Under a longstanding agreement with the United States, the Philippines can request that the United States voluntarily turn over custody of a defendant in a criminal case.

According to Bartelt, the Marine Corps Forces Pacific spokesman, Pemberton will remain in the Philippines, in U.S. custody, during the court proceedings.

“The Marine Corps is working closely and cooperating fully with Philippine authorities to ensure a thorough investigation is completed and due process of law is followed,” Bartelt said.

The Marine Corps, which will pay for Pemberton’s legal representation, has hired a law firm in the Philippines to represent him in this case.

“We look forward to the full cooperation of the U.S. government in ensuring that justice is secured,” Foreign Ministry spokesman Charles Jose said in a statement.

The case is reminiscent of another case in which a U.S. military member was accused and convicted of murder in the Philippines, The Washington Post reported in October:

The murder investigation is drawing comparisons with a 2005 case in which another U.S. Marine, Lance Cpl. Daniel Smith, was accused of raping a Filipino woman in a van near Subic Bay while three other Marines watched and cheered.

Smith was convicted in a Philippine court and originally sentenced to life in prison. He was transferred to the custody of the U.S. Embassy in Manila and detained there until 2009, when his accuser recanted and his conviction was overturned. The outcome stirred suspicion among many Filipinos, in part because U.S. officials granted Smith’s accuser a visa to live in the United States after she changed her story.

Craig Whitlock contributed to this report, which has been updated multiple times.