"Shawki al-Baadani, alias Khawlan al-Sanaani and also Abu Maissara al-Hanki, was left dead by a drone raid" that killed 20 Al-Qaeda fighters this week in the region of Rada, the source told AFP.
The source said that Baadani was among the most wanted leaders of Al-Qaeda in the Arabian Peninsula, or AQAP, seen by the United States as the jihadist network's deadliest branch.
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Baadani was suspected to have been the brains behind a 2012 bomb attack on an army parade which killed nearly 100 soldiers in the capital Sanaa.
The attack was later claimed by Al-Qaeda.
On Tuesday, tribal sources and witnesses reported that twin drone strikes killed at least 20 suspected Al-Qaeda militants near Rada, the focus of deadly fighting between the jihadists and advancing Shiite rebels.
The United States is the only country operating drones over Yemen, but US officials rarely confirm individual strikes.