Emwazi was killed in a us drone strike in 2015, while a fourth member of the cell, Aine Davis, was detained in Turkey.
A US official told the NY Times that the Syrian Democratic Forces (SDF) captured the two in early January in eastern Syria and handed them over to USA authorities in the country. They were known as "The Beatles" due to their British accents.
The Beatles have beheaded more than 27 hostages, according to USA authorities.
A senior USA official confirmed that part of the interrogation of Kotey and Elsheikh is aimed at finding the remains of Western hostages, particularly Americans, who were killed during their ISIS captivity.
Two British Islamic State militants known for their role in the torture and killing of Western hostages have been captured by Syrian Kurdish fighters, according to USA officials.
The New York Times said that the SDF caught the men in January and have made them available to the United States military personnel for questioning.
He gained notoriety by taunting Western government before executing hostages. Both men previously lived in London, and are considered foreign terrorists by the US State Department.
Kotey, who has a Ghanaian and Greek Cypriot background, also grew up in West London.
He was said to be an influential figure in convincing young recruits to travel to Syria and Iraq to join the terrorist organisation.
In March 2017, the State Department sanctioned Elsheikh, saying he was "said to have earned a reputation for waterboarding, mock executions, and crucifixions while serving as an ISIS jailer".