The FBI has confirmed that Marwan, a Malaysian militant, was killed in a raid in the Philippines in January.
Marwan, also called Zulkifli bin Hir, was a leading figure in Islamist militant group Jemaah Islamiyah (JI).
He was believed to have been killed in a raid in the southern Philippines earlier this year that left 44 police commandos dead, but this is the first formal confirmation of his death.
The FBI said forensic evidence had proved conclusive.
"After a thorough review of forensic data and information obtained from our Philippine law enforcement partners, the FBI has assessed that terrorism subject Zulkifli Abdhir [the FBI gives several versions of his name], also known as Marwan, is deceased," it said in a statement quoted by AFP news agency.
He had as a result "been removed from the FBI's list of Most Wanted Terrorists", it said.
Reuters news agency, citing an unnamed FBI source, said the identification was made in part using his severed finger for DNA analysis.
'Got our man'
Marwan was said to have been behind a series of bomb attacks in the southern Philippines since 2006. The US had offered a $5m (£3.2m) reward for his capture.
Jemaah Islamiyah, of which he was a member, has links to al-Qaeda and a long track record of attacks in Indonesia. It is believed to have been behind the Bali bombings of 2002.
The Malaysian militant was killed in a raid on 25 January along with suspected bomb expert Abdul Basit Usman. Both men had been incorrectly reported killed in the past.
The raid has been the subject of considerable criticism in the Philippines, both because of the high police death toll and because critics say it placed a fragile peace process in the restive southern region in jeopardy.
Police entered a town in the southern province of Maguindanao held by the Moro Islamic Liberation Front (Milf), which signed a peace deal with the government last year.
But the rebels say police did not liaise with them about the operation as required under the deal, leading to a clash.
Philippine officials welcomed the FBI confirmation of Marwan's death.
"We have got our man and (the operation) was a success," AFP news agency quoted Philippine national police spokesman Chief Superintendent Generoso Cerbo as saying.