Al Qaeda fighters have made fresh gains in southern Yemen in recent days, as the militant group takes advantage of the country’s eight-month civil war and breakdown of central government authority in a bid to seize territory and extend its influence.

Dozens of militants belonging to Al Qaeda in the Arabian Peninsula, or AQAP, manned checkpoints outside Zinjibar and nearby Ja’ar on Thursday after storming the two cities the previous day, residents and local officials said.

An AQAP announcement broadcast over mosque loudspeakers in Zinjibar declared anyone who keeps their door closed would be safe, a city resident said.

The extent of AQAP’s control over Zinjibar and Ja’ar was unclear, but its advance on the two cities underscores how the Saudi-led military campaign to defeat Iranian-backed Houthi rebels and restore Abed Rabbo Mansour Hadi as Yemen’s president has undermined the fight against Islamist extremist groups in Yemen.

The U.S., in cooperation with Yemeni officials, has carried out an extensive covert program of drone strikes against AQAP leaders in Yemen. The ouster of Mr. Hadi by Houthi rebels in February and the withdrawal of U.S. counterterrorism personnel from Yemen the same month has led to a sharp decline in the strikes, helping Islamic State—as well as AQAP—to flourish.

“AQAP’s capability to gradually expand its geographical reach highlights two things: how the jihadist group continues to be the main beneficiary of the current Yemeni civil war, and how the absence of an effective military force capable to challenge them is granting AQAP an almost complete freedom of maneuver across much of southern Yemen,” said Ludovico Carlino, a senior analyst at IHS Country Risk.

Control of Zinjibar, the capital of Abyan province, has been contested since Arab Spring protests against longtime President Ali Abdullah Saleh spread across Yemen in early 2011. After changing hands several times between Yemeni government forces and AQAP fighters in 2011 and 2012 then falling under the sway of Houthi rebels earlier this year, the city was seized in August by local militias allied to Mr. Hadi.

In the latest fighting, AQAP drove out the militias, known as Popular Committees, and killed their deputy commander Ali al-Sayed when they took over Zinjibar, residents said. The defeated fighters fled to Aden, the southern port city where Mr. Hadi’s government is currently based.

In a Twitter post on Thursday, Yemen’s al Qaeda affiliate accused Mr. Sayed of ties to the U.S. drone campaign, according to the SITE Intelligence Group.

AQAP’s push on Zinjibar and Ja’ar, 9 miles to the north, follow its seizure of the southern coastal city of Al Mukalla in early April, a few days after Saudi Arabia assembled a military coalition of mostly Gulf Arab allies to take on the Houthis.

After relying exclusively on airstrikes, the coalition has added ground forces to what has become an unexpectedly protracted military campaign against the Houthis, a Shiite group whose stronghold is in northern Yemen. The U.S. supplies the coalition with logistical and intelligence support.

Iran, Saudi Arabia’s main regional rival, says the Houthis should have a role in governing Yemen but denies supplying them with weapons.

WSJ