Abdullah Al Senussi, the former head of intelligence under Muammar Gaddafi, was captured Sunday in southern Libya, according to reports.
Senussi, who was also Gaddafi's brother-in-law, was arrested at his sister's house in the desert town of Birak, military commander Ahmed al-Hamdouni told Reuters.
Hamdouni said soldiers found Senussi thanks to information from residents of the area, which is near where Saif al-Islam Gaddafi was captured Saturday.
Officials from the military and the National Transitional Council confirmed the arrest, reported Agence France Presse.
Senussi is being held in custody in Sabha and will be taken to Tripoli to face trial, NTC official Mohammed Sayeh told CNN.
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The International Criminal Court issued a warrant for Senussi's arrest in June. He was the last Libyan wanted for war crimes still at large, after the capture of Saif.
Like Saif, Senussi was believed to have fled to Mali or Niger following the death of Muammar Gaddafi, though some reports had suggested he was dead.
The Tripoli Post describes Senussi as "one of the most feared and influential of Muammar Gaddafi's men."
He was one of the former leader's most trusted aides, said the BBC, and also served as an advisor to Saif al-Islam.
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Senussi was blamed for mass deaths in the eastern city of Benghazi during Libya's revolution, according to the Guardian, and is said to have recruited foreign mercenaries to fight for Gaddafi's regime.
He is equally accused of human rights abuses dating back before the revolution, including the massacre of more than 1,000 inmates at Tripoli's Abu Salim prison in 1996.
He is alleged to have organised an attack on a French UTA passenger plane in 1989 in which 170 people were killed, said AFP, for which a Paris court found him guilty in absentia.
Senussi is also thought to be behind an alleged plot to assassinate Crown Prince Abdullah of Saudi Arabia in 2003.
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