The extremists on Sunday "placed the woman in a hole in the middle of the courtyard of a military building and stoned her to death in the presence of dozens of residents" of Hadramawt provincial capital Mukalla, one witness said.
A local journalist at the scene confirmed the rare stoning, saying that the gunmen prevented photography of the execution.
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"This was the first time we have seen such a thing," another witness said.
A copy of the purported verdict issued by the so-called Hadramawt court of al Qaeda's Ansar al Sharia in December said the married woman "confessed in front of the judges to committing adultery".
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Al Qaeda's Yemen branch is considered by Washington to be the most dangerous affiliate of the global network.
It has taken advantage of the state's weakness to expand its control in various areas, including the vast Hadramawt region.
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