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“Zeidan’s ouster is significant because it could lead to further turbulence,” said Frederic Wehrey, a senior associate in the Middle East program at the Carnegie Endowment for International Peace.

Since Gadhafi was toppled, a hodgepodge of rebel groups — some of which participated in the revolution — has carved up Libya into personal fiefdoms or what William Lawrence, a senior fellow at the Project on Middle East Democracy, describes as “a confederacy of armed groups and a municipality-based set of militias.”

While the Libyan government has sought at times to assert itself, it is the rebels who have repeatedly reclaimed the upper hand.

Rebels on the government payroll briefly took Mr. Zeidan hostage in October. This month, armed men attacked the Libyan parliament and forced it to relocate to a hotel in Tripoli.

Sunday’s mission may have only worsened the U.S. position with the increasingly powerful rebel groups. A militia commander controlling Libya’s oil terminals denounced the U.S. and condemned the SEAL mission, saying Tuesday that Washington was siding with Tripoli against the aspirations in the eastern half of the country for greater autonomy.

The Associated Press reported that Ibrahim Jedran, the 33-year-old militia commander who organized the forces that took control of Es-Sider from the central government, said Washington was aligning with the wrong side in the dispute over Libya’s future. He said in an interview on a rebel-controlled television network that the central authorities in Tripoli and the country’s parliament are dominated by Islamists and ignore the aspirations of the country’s eastern regions.

“The free world should stand next to the side of truth,” Mr. Jedran said. “But today we find a superpower declaring piracy.”

The U.S. had acted at the request of the Libyan and Cypriot governments.

The threat posed by the militias is worrisome, but “the saving grace is that there has always been a balance of weakness on the ground and not one rebel group is able to fully dominate the others or control the government,” Mr. Wehrey said.

Al Qaeda affiliates take hold

Awash with weapons, many of them taken from Gadhafi’s stockpiles, Libya has turned into an arms black market that is fueling conflicts not just in Libya, but across the region.

A United Nations panel on Libya found widespread trafficking over the past year of shoulder-launched anti-aircraft missiles from Libya to Mali, Chad, Tunisia, Lebanon, Syria, Egypt and the Gaza Strip.

The Libyan government’s lack of oversight of its weapons and its inability to control key ports and borders, coupled with the fact that non-state groups control most of the weapons, have increased the risk that these arms will fall into the wrong hands, said Mr. Katulis, who served on the U.N. panel that produced its report in February.

The report also found that “a complicated mix” of al Qaeda-affiliated and -inspired groups, including Ansar al-Sharia and elements linked to al Qaeda in the Islamic Maghreb, have flourished amid the lawlessness in many parts of Libya. Ansar al-Sharia was one of the groups linked to the September 2012 assault in Benghazi.

The U.N. panel’s report cited the capture of a prominent Islamist militant leader, Nazih Abdul-Hamed al-Ruqai, also known as Anas al-Libi, by U.S. special operations forces in Tripoli in October as evidence of “the attraction Libya holds for terrorist groups.”

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