The unidentified junior-enlisted Marine was taken into custody at the San Ysidro port of entry near San Diego around 1:30 p.m., Marine spokesman Lt. Cameron Edinburgh said in a statement to Fox News.
The 20-year-old is assigned to the 1st Marine Division’s headquarters battalion at Camp Pendleton, Calif.
Customs officials found the two women in the trunk of a 2007 Ford Mustang when the Marine was pulled aside for additional screening. Customs and Border Patrol officials are investigating the incident.
"The Marine is currently being held in civilian custody.," Edinburgh said."The determination as to the adjudicating authority has not yet been made."
The Marine is expected to face federal charges, a CBP spokesperson said.
Edinburgh said the Marine has not served in the Southwest Border Support Mission, where U.S. troops are assisting border agents on the U.S.-Mexico border.
Monday's arrest comes as several other Marines stationed at Camp Pendleton are facing human trafficking charges. Six out of two dozen Marines recently pled guilty to human trafficking and drug charges at military court-martials.
Sixteen of the Marines charged were arrested in July during a battalion formation that has since been ruled unlawful and a violation of their rights. Charges against them were later dropped.
In July, Border Patrol agents arrested two Marines, Lance Cpl. Byron Darnell Law II and Lance Cpl. David Javier Salazar-Quintero near the border when they were caught with three undocumented immigrants in the back seat of their vehicle.