The power struggle could distract his Taliban forces along the Afghan border from their spring offensive against US and allied troops.
Mr. Mehsud commands one of the three major pockets of Taliban fighters in Pakistan. His rugged domain here in South Waziristan provides a launch pad for cross-border attacks into southern Afghanistan and a suspected hideout for Al Qaeda figures.
His new adversary, Qari Zainuddin Mehsud, has joined forces with another splinter group and has dispatched his men to cut off Baitullah's movements and foment a popular uprising against him.
"I think Baitullah Mehsud is feeling constrained by this," says Mahmood Shah, Pakistan's former security chief of this lawless border region known as the Federally Administered Tribal Areas (FATA). Zainuddin remains less organized than Baitullah, says Mr. Shah, but he is gaining in momentum and popularity among the local fighters.
The rupture raises the prospect that tribal rivalries could be exploited to sap the Taliban movement. But analysts warn that there are limits to a divide-and-rule strategy given the way the Taliban have undermined tribal power structures – and resisted meddling by Islamabad or Washington.
"When a group gets government patronage it gets discredited, so I think for some time the group should be left on their own," says Shah. "If [outside governments] have to do it, they should do it very secretly."
Two subtribes, one full-blown feud
This particular rift between Zainuddin and Baitullah dates back to March 2008. Assailants in the town of Tank killed Muhammad Yousaf, a prominent elder of the Shamenkhel subtribe and Zainuddin's uncle. The Taliban have been known to target tribal elders in an effort to seize power. Soon after, gunmen shot dead Baitullah's younger brother, Yahya Khan Mehsud.
Until this incident, Zainuddin had been a leading member of Baitullah's fighting force. Now tit-for-tat killings have sowed the seeds for a full-blown blood feud between the two men and their subtribes.
Baitullah warned his rival to "be ready for a bloody clash" after an Apr. 15 deadline for surrender passed, in a message passed to Zainuddin through tribal elders. "Neutral members of the population should stay indoors, because everyone who gets in our way will be crushed," he threatened.
Such tough talk has become the norm between the two men, whose forces have clashed on and off over the past year.
Late last month, Zainuddin's men distributed pamphlets in Tank, a gateway to the embattled South Waziristan, where many locals have fled, encouraging them to join him in trying to oust Baitullah Mehsud from the region.
"Baitullah runs a terror network and a death squad," the pamphlet said. "He has slaughtered up to 283 tribal elders who were opposing him and killed lot of religious leaders. Come forward, my clansmen, to force him out of the once peaceful South Waziristan."
Shah says that Zainuddin has tried to pick away at Baitullah's Islamic credentials by asking how it's right to be fighting the Army of Pakistan, a Muslim nation.
But it would be a mistake to see Zainuddin as some sort of moderate, argues Ijaz Khan, a professor of international relations at the University of Peshawar. "He is a militant. He is as much a Talib as Baitullah," says Mr. Khan.
Keeping Baitullah busy
Yet Zainuddin does have the potential to keep Baitullah busy with a serious showdown. A Pakistani intelligence official estimates Zainuddin's strength at about 2,000 to 3,000 fighters, while Baitullah, who until recently had the support of 10,000 to 13,000, these days is losing men. A head-on fight would create "unspeakable" trouble for Baitullah, says former ambassador to Afghanistan Rustam Shah Mohmand, because Zainuddin also enjoys greater support from the local population.
"If the clash happens between Baitullah Mehsud and Qari [Zainuddin], then it will lead to greater mayhem among the Taliban ranks elsewhere in the Pakistani tribal region," says Mr. Shah, the former FATA chief.
That would be welcome news for Pakistani forces battling Baitullah, whom the government blames for the 2007 assassination of former Prime Minister Benazir Bhutto as well as a recent attack on a police academy in Lahore. Some here believe that the government is secretly supporting Zainuddin for this reason.
Shah doubts US-led forces in Afghanistan would see much change if Baitullah were distracted from fighting them because he says the Pakistani Taliban's reach across the border is overhyped.
But grooming rivals may backfire
Even if such tribal infighting does benefit American and Pakistani troops in the short term, some analysts argue against Washington and Islamabad encouraging such rifts.
"This strategy may appear to give you short-term gains, but I think over the intermediate term we may see many warlords and groups coming up turning around against the government and make a much worse situation," says Mr. Khan.
On top of this concern, Khan says the Taliban have irrevocably weakened the traditional tribal system of elders: "If the Taliban already targeted the tribal elders, you cannot create new tribal elders."
He argues, instead, for bringing modern state institutions – security forces, courts, and political parties – into this region, which until now has been afforded great autonomy.
Others say that over time new leaders could emerge by a gradual process of reputation building, but it requires the fear of the Taliban to be lifted. Popular disenchantment with the Taliban may be helping that process along, and could explain some of Zainuddin's emerging strength.
"After having been in the Taliban system for two years, slowly people are starting to feel an aversion to that system, and they think the old system was probably better," says Shah.