Witnesses said al-Qaeda gunmen in the southern city of Mukalla read out charges before shooting the two men, one of whom was accused of guiding the US drone that killed commander Nasr al-Ansi and a media liaison known as Muhannad Ghalab in April.
Al-Qaeda supporters posted pictures online that showed the two men blindfolded on a sandy beach, said to be the site of a previous drone strike.
The killings came a day after al-Qaeda in the Arabian Peninsula, as the Yemeni affiliate is known, said its leader, Nasir al-Wahishi, was killed in a US drone strike last week.
Al-Qaeda captured Mukalla in April after Yemen's army splintered between allies and opponents of Shiite rebels known as Houthis, who captured the capital last year.
But the city has proven to be something of a death trap, with US drone strikes in and around Mukalla killing not only al-Wahishi and al-Ansi, but also a senior religious ideologue, Ibrahim al-Rubaish.
They identified him as Musaed al-Khaweitar, saying he ran an al-Qaeda-linked media outlet and was close to top leaders. The second man, identified as Abu Ayman al-Mutairi, is also believed to be Saudi.
AQAP is widely seen as the terror network's most dangerous offshoot, and claimed the attack on the offices of French magazine Charlie Hebdo in January, which killed 12 people. It has also been linked to a number of attempts to attack the United States with bombs snuck past airport security.
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