Hakimullah Mehsud and Waliur Rehman will share control, but analysts say infighting could erupt again.
The arrests show that militants still pose a threat throughout the country despite the death of Taliban leader Baitullah Mehsud.
A council picked Hakimullah Mehsud to head the alliance, two days after another senior figure said he had taken over. The announcements may signal infighting, which in recent weeks has led to bloody clashes.
Unmanned aerial drones have become important weapons in the US counterterrorism effort. But questions are mounting about who controls the drones, and what laws govern their use.
Meanwhile, another US airstrike on South Waziristan – like the one that targeted Baitullah Mehsud – killed 10 suspected militants Tuesday.
A reported shootout over who will succeed Baitullah Mehsud as chief may have killed one top candidate and critically injured another.
He rejects Bush's 'global war on terror' as too absolutist. But a top adviser says Obama will 'confront Al Qaeda aggressively wherever it exists.'
The targeting of the Pakistan Taliban leader showed US willingness to pursue Pakistani priorities. The US may now push for more help in finding Pakistan-based militants who operate in Afghanistan.
Without the charismatic Baitullah Mehsud, feuding Islamist militants could splinter.