Last year Al Qaeda and and its local affiliate in Yemen, Ansar al-Sharia, succeeded in doing something they had never been able to do before: They boldly seized control of territory in southern Yemen — without resistance from the Yemeni army — and declared several cities, including Ja’ar and Zinjibar, “Islamic Emirates.”

In last month’s report Al Qaeda in Yemen, award-winning reporter Ghaith Abdul-Ahad journeyed to Ja’ar and other Al Qaeda-controlled areas in the south to investigate how Ansar al-Sharia has been running whole towns and cities, and working to win the hearts and minds of the local population by administering scarce resources like water and electricity.

But today the Yemeni Defense Ministry announced that the Yemeni army, which intensified its U.S.-backed campaign in the south last month, has retaken both Zinjibar and Ja’ar, and driven the militants from the cities.

“I am now speaking from the local government headquarters in Zinjibar,” Major Gen. Salem Qatan, commander of the southern region, told Reuters. “The cities of Zinjibar and Jaar have been completely cleansed.”

A spokesperson for Ansar al-Shariah also confirmed to Reuters that the army had retaken control of Ja’ar, and residents reported that “militants had left behind flyers asking inhabitants to forgive them, asserting that they had not wanted to ’cause any harm to Ja’ar and its inhabitants.'”

Madad News Agency, Ansar al-Sharia’s media wing, claimed on its Facebook page that Ansar had withdrawn from the areas in order to protect the local population from the army’s shelling.

But Mohammed Albasha, the spokesperson at the Yemeni Embassy in the U.S., told FRONTLINE the note was an attempt to save face. “They rarely acknowledge defeat,” he said.

“It was going to happen sooner or later,” Albasha said, referring to the recapture of the two cities. “Al Qaeda realized their tactics — holding ground — is not a viable option.” But he also cautioned that the victory doesn’t spell the end of Al Qaeda or Ansar al-Sharia.

“Our fear is that they will go back to old tactics, like suicide attacks and hit and runs [attacks],” he said. “We still have two areas, Azzan and Shaqra, where Al Qaeda exists, and there are still probably pockets in Zinjibar and Ja’ar, where they may be hiding.”

Update

June 15, 2012: The Yemeni Army declared the port town of Shaqra cleared of Al Qaeda today, which according to Reuters, “puts an end to their short reign in Abyan [province], during which they governed large swathes of the province according to strict Islamic sharia rules.” Yemeni Defense Minister Major-General Muhammad Nasir Ahmad told Reuters the military’s new goal was to recapture Azzan.