Indonesia-born Hambali has been dubbed by the US Central Intelligence Agency the "Osama Bin Laden" of South East Asia.
Hambali is suspected of playing a leading role in the Bali bombing
He is believed to have been the operations chief for the shadowy militant group Jemaah Islamiah (JI), and has been named as a key suspect in a string of bombings across the region.
The Islamic scholar, whose real name is Riduan Isamuddin, is wanted by Indonesia, Malaysia, Singapore and the Philippines in connection with a series of bomb attacks.
He is also accused of arranging a meeting between two of the 11 September hijackers with other al-Qaeda figures in Malaysia in January 2000, and of being behind other plots to blow up Western targets in the region.
And he is further accused of connections with the suspects accused of bombing the USS Cole in Yemen in October 2000.
He has faced lengthy interrogation by the US following his arrest, in central Thailand in 2003. He has now been sent to Guantanamo Bay, Cuba.
JI is blamed for several attacks across South East Asia, including the 2002 Bali bombing, which killed 202 people, and the 2003 attack on the Marriott hotel in Jakarta, which killed 12.
Analysts say JI wants to establish an Islamic state across Malaysia, Indonesia, Singapore and parts of the Philippines.
Indonesia's civilian intelligence service has linked Hambali specifically with the 2002 Bali attack.
He is thought to have been the major brains behind the operation, as well as the financial conduit.
Indonesia's Defence Minister, Matori Abdul Djalil, has said that Hambali was deputy to Abu Bakar Ba'asyir, JI's alleged leader.
Abu Bakar Ba'asyir was jailed in 2005 after he was found guilty of conspiracy in connection with the 2002 Bali attacks. He denies any links with JI.
Hambali was born in West Java in 1966, one of 13 children in a poor family.
As a teenager he became involved in a network of local groups known broadly as Jemaah Islamiah, which literally translates as "Islamic community". One of the men allegedly running the network was Abu Bakar Ba'asyir.
Hambali became involved in radical Islam as a reaction against the religious repression of the Suharto regime throughout the 1970s and 1980s. In 1985, when Hambali was aged 19, he sought exile in Malaysia, along with Mr Ba'asyir and other followers.
From there he travelled to Afghanistan in 1988 to fight as a Mujahideen guerrilla against Soviet occupation.
He returned to Malaysia in 1990, where he is believed to have travelled the country recruiting young Muslims to join a jihad (holy war) with the eventual aim of setting up a pan-Asian Islamic state.
Back in Indonesia, Suharto was overthrown in 1998, and Hambali is believed to have returned there in October 2000 to recruit more supporters.
On Christmas Eve that year, a series of bombs exploded almost simultaneously in nine Indonesian cities, many of them in churches. Eighteen people were killed.
A series of suspects have named Hambali - who returned to Malaysia a few days before the attacks - as the mastermind for the bombings.
A few days after the Indonesian bombs, 22 people were killed in a series of simultaneous bombs in the Philippine capital Manila. Philippine police say they have evidence that Hambali funded the attacks.
Philippine prosecutors have charged Hambali in absentia with involvement in a plot to smuggle explosives from the Philippines to Singapore in 2000, for an attack on US and Israeli targets, which was foiled.