The official named the two dead men as Gazwan al-Waili and Zubeir al-Sanaani and said "they were known for their links to Al-Qaeda".
After Yemeni government forces retook Hadramawt provincial capital Mukalla in the southeast on April 24, after Al-Qaeda had held it for a year, the jihadist fighters headed north to Marib province.
Washington, which views Al-Qaeda's Yemen-based branch as its most dangerous, acknowledged on May 7 that a "very small number" of US military personnel has also been deployed in support of the operation to retake Mukalla.
The United States regularly conducts air strikes against Al-Qaeda. A March strike on a training camp west of Mukalla killed more than 70 fighters.