Abdel Hakim Belhaj, commander of the Tripoli Military Council, is now responsible for keeping order in Tripoli. He was formerly the emir of the Libyan Islamic Fighting Group, which was considered a terrorist organization by the United States. (Daniel Berehulak/Getty Images)

— For decades, bearded men in Libya were afraid to walk in the streets or go to the mosque, worried that to be seen as an Islamist would land them in prison, or worse.

As Libya’s leader, Moammar Gaddafi regarded Islamists as the greatest threat to his authority, and he ordered thousands of them detained, tortured and, in some cases, killed. The lucky ones fled the country in droves. But with Gaddafi now in hiding, Islamists are vying to have a say in a new Libya, which they say should have a system based on Islamic law.

Although it went largely unnoticed during the uprising that toppled Gaddafi last month, Islamists were at the heart of the fight, many as rebel commanders. Now some are clashing with secularists within the rebels’ Transitional National Council, prompting worries among some liberals that the Islamists — who still command the bulk of fighters and weapons — could use their strength to assert an even more dominant role.

“We don’t want any vacuums or for those Islamists to steal the revolution,” said a senior rebel leader, who spoke on the condition of anonymity to discuss the internal rifts.

Among the Islamists in the rebel ranks, a small fraction were militants who had previously waged war abroad. Some had fought in Afghanistan, Iraq, Chechnya and the Balkans under a religious banner; some had ended up in the arms of more extreme groups such as al-Qaeda. The city of Derna, a key bastion of resistance against Gaddafi in eastern Libya, was home to dozens of Libyan fighters who fought in Iraq after the 2003 U.S.-led invasion.

In the fight against Gaddafi’s troops, the Islamist militants played an important role among the rebels’ ragtag forces because of their experience in battles overseas. With a place in the new Libya, most have said that their days as militants are over. The largest of the organizations, the Libyan Islamic Fighting Group, has rebranded itself as the Libyan Islamic Movement for Change.

Some Islamists are blunt in expressing resentment about fellow rebels.

“Secularists don’t like Islamists,” said Ismail Sallabi, an influential cleric who is among nine leaders commanding rebel forces in eastern Libya. Before the revolution, he said, he had never held a weapon. “They want to use Islamists in the fighting stage and then take control.”

“I’m proud to be an Islamist, and this is a historic chance for the West to understand Islamists up close,” Sallabi said.

Seeking a compromise

Libya is a conservative Muslim nation, and its future government will probably reflect that; the governments of Egypt and Iraq are among Arab states that base their governance on Islamic law. Although Gaddafi’s government tolerated little in the way of activism, Libya’s Islamist groups appear to have emerged from his reign as the best-organized among political groups, and secularists among the country’s new leaders appear determined not to alienate them.

In an early step intended to rein in Islamists, Libya’s new leaders have created a Supreme Security Committee, which has put the most powerful rebel commander, former militant Abdulhakim Bel­hadj, under civilian control. But in an interview, Ali Tarhouni, a liberal who heads the committee, also sounded a conciliatory note.

The Libyan Islamic Fighting Group is “not al-Qaeda. They don’t have any intention of fighting the West or Europe. This is a group that basically carried arms to topple Gaddafi’s regime,” Tarhouni said. “Their brand of thinking is not geared towards the instability of the rest of the world.”

Even before Gaddafi’s ouster, Islamists and secularists on the Transitional National Council clashed this summer on whether Islamic law should be the primary source for legislation. Initially, secularists prevailed, winning approval of a provision that established Islamic law as one guidepost for a future Libya, but not the dominant one.

Days later, however, Islamists led by the Libyan Muslim Brotherhood took advantage of secularists’ absence from the eastern city of Benghazi to win passage of a revised provision that made Islamic law the principal law of the land, said a council member involved in the process. He spoke on the condition of anonymity to discuss the fraught subject.

One prominent Islamist, Abdul Razag el-Aradi, a nationalist who is close to the Muslim Brotherhood, described that approach as a compromise intended to appease more conservative Islamists while stopping well short of an approach that would transform Libya into an Islamic republic.

“There are two kinds of people we in Libya will completely reject: extremist Islamists and extremist secularists,” Aradi said.

Criticism of rebel council

But some Islamist commanders are pushing for further change. They have expressed anger about the role of the civilian government, which includes many who spent the past few months traveling abroad while fighters — a mix of young and old, secularists and Islamists — were entrenched in a brutal battle with Gaddafi’s forces.

In Benghazi, Sallabi, the cleric who is part of the rebel command, has called for the resignation of the council, saying that its efforts to unfreeze assets held in Western countries produced little in the way of money for the fighters.

Sallabi spent years in Tripoli’s Abu Salim prison, where he was tortured, he said, because he and his family members are Islamists. He never wants to be targeted for his beard and his beliefs again, he said. His brother, Ali Sallabi, is emerging as an important figure in the Muslim Brotherhood, one who has contributed to the constitutional charter and is seen as a spiritual leader for some of the fighters. Ali Sallabi has also been sharply critical of Prime Minister Mahmoud Jibril’s leadership, complaining that he has embraced too secular an agenda and is too often out of the country.

“We want this to be a good government that comes from Islam, that respects human rights and personal freedoms,” Ismail Sallabi said in an interview in Benghazi last week. “Doctor Ali will do his best to give Libya to trusted hands,” he said, referring to his brother.

Military commanders estimate that 50 to 70 percent of the rebel fighters have Islamist roots and say that Islamist leaders will need to be given a prominent role in the next government. Some say the estimate is exaggerated. Many rebel fighters interviewed said Islamists may have taken leadership roles but are in the minority. Those rebels vowed to turn on the Islamists if they seize control.

Among the Islamist fighters was Abdul Basset Haroun al-Shahaidi, who lived in exile for 21 years because of his family’s opposition to Gaddafi. He has traveled abroad to seek money for security training in Libya, and he says Western officials have quizzed him about the rise of Islamists within the new Libya.

“The Islamic way is not something dangerous or wrong. The West hears ‘Islamic law’ and they think we want to lock our women in boxes,” Shahaidi said. “The Islamic groups want a democratic country, and they want to go to the mosque without being arrested. They’re looking for freedom like everyone else.”