Ayombekov, whose forces clashed with government troops this week—a battle that killed more than 40—typifies the shadowy figures that have tormented authorities in Tajikistan, a country whose obscurity and poverty belie its strategic significance.
Battles with groups such as Ayombekov's threaten the stability of a country that is important to U.S.-led military operations in Afghanistan and that is a main transit route for opium destined for Russia and Western Europe. Observers also worry that an eruption of sustained violence in Tajikistan could trigger unrest in neighboring Kyrgyzstan and Uzbekistan, which also are key countries in the Afghan campaign as routes for military supply and withdrawal.
Tajikistan's security woes date back to the 1991 breakup of the Soviet Union, when rival political groups jockeyed for power in violent street conflicts that burst into full-fledged civil war in 1992. More than 60,000 people are estimated to have been killed before an uneasy peace deal was reached in 1997.
Under the U.N.-brokered deal, 30 percent of government posts were to be allocated to members of the United Tajik Opposition, an eclectic alliance that brought together Islamists, nationalists and democrats.
Since then, authoritarian President Emomali Rakhmon's government has diluted the terms of the agreement, pushing UTO members out of state positions and bolstering control over regions. Rakhmon's two decade-long rule has been marked by persistent violations of democratic standards and suppression of political opposition.
Ayombekov, 46, was a rebel leader during the civil war and was later appointed a commander of the border police on a section of Tajikistan's 1,200-kilometer (750-mile) frontier with Afghanistan. But observers say he and his forces exert strong informal influence over his native Gorno-Badakhshan region, where deeply impoverished villages nestle among some of the world's highest mountains.
The warlord culture is extensive in Tajikistan, reflecting how local loyalties trump trust of the government and the desire of impoverished men to find income outside legal means.
Authorities accuse Ayombekov, the suspected ringleader of a tobacco-running operation, of being behind last week's murder of Abdullo Nazarov, a general in Tajikistan's national intelligence service. Although only Ayombekov and three others are being sought for the killing, hundreds of troops have reportedly poured into Khorog, the capital of Gorno-Badakhshan, to hunt them down.
Speaking with The Associated Press by telephone before fighting broke out, Ayombekov said the security operation was aimed purely at rounding up former civil war commanders. He denied having anything to do with Nazarov's death.
Rakhmatillo Zoirov, who leads the opposition National Social Democratic Party, said he did not believe the government account of events that led up to this week's clashes.
"The military operation in Khorog was nothing other than a decision by the authorities to once and for all get rid of Badakhshan's informal leaders—the former field commanders and fighters in the United Tajik Opposition," Zoirov said.
Eliminating former armed opposition leaders, many of whom are suspected radical Islamists, has emerged as a recurring policy in the government's strategy to take the whole country back.
In 2009, under the guise of a drug eradication drive, the army launched a military operation in the Rasht district, once a UTO stronghold, that culminated in the capture of several foreign fighters and the killing of former opposition commander Mirzo Ziyoyev.
Another influential Rasht-based ex-warlord, Mirzokhodzha Akhmadov, later managed to defy government efforts to capture him and surprised many by brokering a murky deal with the authorities that has guaranteed his continued freedom.
Tajikistan's presence in a dangerous neighborhood makes the prospect of continued unrest an alarming one.
Russian analysts closely follow events in the former Soviet state, which is currently embroiled in tense negotiations over a military base lease with Moscow, and have been predicting a possible downward spiral of instability across Central Asia after the U.S. withdrawal from Afghanistan starting in 2014.
Vladimir Zarikhin, deputy director of the Moscow-based CIS Institute, said it was incumbent on President Rakhmon to gain effective control over Gorno-Badakhshan, which covers around half the country, to avoid a descent into complete collapse.
"He is perfectly entitled to do that, since he understands that if he doesn't take complete control before the withdrawal of troops from Afghanistan, he could lose that half of the country," Zarikhin said.
Leonard reported from Almaty, Kazakhstan.