Yemen's Defense Ministry confirmed the deaths of the brothers in Shabwa province, but would not provide any further details.
In September, the country's foreign minister said it was no longer allowing missile strikes by pilotless planes, however after Al Qaeda smuggled explosives aboard cargo planes bound for the U.S. in late October, it is believed the strikes resumed after a yearlong hiatus.
Yemen, which is currently wracked by popular protests against the country's deeply unpopular president, is also home to one of the most active branches of Al Qaeda, which has planned several attacks against the U.S.
Shabwa provincial security and tribal officials reached by telephone identified the two brothers as Abdullah and Mosaad Mubarak, but they did not explain why they were sure the attacks were carried out by pilotless aircraft.
The officials spoke on condition of anonymity because of the sensitivity of the incident.
Al Qaeda in the Arabian Peninsula, as the local branch calls itself, is estimated to number around 300 fighters with built up strongholds in the provinces of Shabwa, Abyan, Jouf and Marib, regions of daunting mountain ranges where central authority has nearly no presence.
In addition to attacking government targets, the group has inspired attacks by Muslims inside the United States and twice smuggled explosives aboard aircraft headed to America.
The U.S. originally carried out a campaign of drone strikes similar to the one that killed so many Al Qaeda figures in Pakistan until a local official was accidentally killed. In September 2010, Foreign Minister Abu Bakr al-Qirbi said the strikes had been suspended.
The U.S. has poured money into training Yemeni counter-terrorism forces with $150 million in annual military assistance and up to 100 trainers at any given time.
The popular protests calling for the ouster of long-serving President Ali Abdullah Saleh across the country, however, has disrupted government efforts against Al Qaeda.