Marwan, whose real name is Zulkifli bin Hir, was believed by the FBI to a member of southeast Asian terror group Jemaah Islamiyah's central command.
The FBI said in February that a DNA sample -- understood to be from a severed finger -- taken from a man killed in a raid in the southern Philippines showed a link with a known relative of Marwan.
But the FBI now says tests have confirmed that the dead man was the wanted Islamic extremist.
"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 ... is deceased and has been removed from the FBI's list of Most Wanted Terrorists," David Bowdich, assistant director in charge of the FBI's Los Angeles field office, told CNN in a statement.
The FBI had been offering a $5 million reward
for information leading to Marwan's capture in the wake of his 2007 indictment on terror charges in a California court.
It accused him of being a supplier of IEDs to terrorist organizations, and having conducted bomb making training for terror groups, including the Philippines-based Abu Sayyaf.
Marwan had previously been falsely reported dead after a raid by Philippine security forces in 2012.
The Philippines has been fighting an insurgency in the predominantly Muslim south for years, and last year signed a peace agreement with the Moro Islamic Liberation Front (MILF), the largest rebel group in the region.
But in January it launched a surprise raid in pursuit of Marwan at Mamapasono, in the southern province of Maguindanao.
The mission went disastrously awry.