In this Feb. 2, 2001 file photo, rebel Commanders Alfonso Cano, left, and Ivan Rios, right, commanders for the Revolutionary Armed Forces of Colombia, or FARC, give a news conference in San Vicente del Caguan, in the rebel controlled area in southern Colombia. (Scott Dalton/AP)

— The death of the supreme commander of Colombia’s main rebel group leaves his organization temporarily rudderless, its far-flung units ever more disunited and its commanders painfully conscious of the improved capabilities of the armed forces, analysts and government officials said Saturday.

Guillermo Saenz Vargas, the Bogota intellectual who fled to the mountains to become a revolutionary, was killed Friday in a shootout with elite commandos after a months-long pursuit.

In a telling footnote, the guerrilla commander died in a rugged region of southwest Colombia that was far from the area where he normally operated, with the state’s intelligence apparatus pinpointing his whereabouts with the help of informers within his own rebel group, military officials said.

The rebel leader, widely known to Colombians by the alias Alfonso Cano, was apparently shot three times outside a small house hours after an aerial bombardment had flushed him from a guerrilla encampment, the military reported. His death leaves the other six members of the group’s ruling circle, the secretariat, with the challenge of choosing a leader who can both command respect and unite a waning fighting force accused of trafficking cocaine to the United States.

Since 2008, aerial bombardments have killed two members of the secretariat of the Revolutionary Armed Forces of Colombia, or FARC, dozens of guerrillas have been deserting every month, and the group’s ability to hold territory has been sharply diminished.

“This is a major blow, the most important against the FARC because of the importance that Alfonso Cano had within the rest of the secretariat,” President Juan Manuel Santos told reporters Saturday afternoon at the scene of the military operation. “What many analysts had said was if Alfonso Cano were killed he would be irreplaceable.”

In urging FARC members to join a government-run disarmament program, the president noted that Cano could not be saved by several rings of rebel security specialists. “This can serve as a warning: No member of the FARC can be safe in any corner of the country,” Santos said.

Analysts said Cano’s sudden departure from conflict, which began in 1964 with the FARC’s birth, poses a difficult test for a rebel group with national pretensions. Some observers who have closely tracked the FARC believe Cano’s death could in time lead to a fragmentation within the group’s many units.

“This is the beginning of them being less of a national organization,” Adam Isacson, an analyst with the Washington Office on Latin America, said by phone from northern Colombia. “There’s going to be tremendous centrifugal forces inside the FARC, with the units that are the biggest and with the most money looking for ways to distance themselves.”

Rodrigo Rojas, who worked to disarm smaller rebel groups in the past, said Cano had not fully consolidated himself because he had only been commander since 2008, when the rebel’s founder, Manuel Marulanda, died of a heart attack. Cano, meanwhile, has been more focused in recent months on just “trying to keep from getting himself killed,” said Rojas, who works with rural communities in war zones with the Catholic group Pax Christi Netherlands.

“So, the vacuum left by Marulanda has never really been filled,” Rojas said.

Those who know the FARC’s leaders intimately, however, note that the group has throughout its history been able to overcome the loss of important commanders. Camilo Gomez, a former peace commissioner who tried to negotiate an agreement with the group, noted that the FARC has never depended on one messianic figure.

“Remember, for the FARC, the death of a guerrilla is natural, it is something that happens, a byproduct of the conflict,” Gomez said.

Aldo Civico, a conflict resolution specialist at Rutgers University, said the group still has significant capacity to carry out military operations in some regions of the country. And the group has been aggressively working to recruit disenfranchised urban youths, including university students, said Civico, who frequently carries out research here.

Still, Civico said that FARC leaders must be aware of the growing futility of their struggle. If a more politically minded commander rises to the leadership position, Civico said, it could mean changes in the group’s strategy.

“I see this as a game changer because it could lead the FARC to realize that the armed struggle is not bringing victory to them and could lead them to negotiations,” Civico said.

Cano, in his public comments and actions, had shown himself committed to the FARC’s goal of taking power by force. “For the long term, we have it defined: We want to be in power,” he told The Washington Post in a one-on-one interview in 2000.

Still, facing an increasingly untenable situation, the FARC had in recent months sent out signals that some analysts believed showed a new willingness on the part of the group to consider negotiations. In January, Cano had said in a statement that compensation to victims of Colombia’s war — a central feature in a law pushed by Santos — was “essential to a future of reconciliation.”

But the Colombian government had long insisted that it would only engage in talks with the FARC as long as the group called a cease fire and released the hostages it holds in jungle camps. Those demands have continued to be rejected by the group.

On Saturday, Santos again said that the possibility of a negotiated, peaceful solution to the conflict was not “under lock and key.”

“But I insist, we need very clear signs,” Santos said. “And we need that they end the terrorism . . . . This organization is all the time weaker because politically they’re defeated. Ninety-five percent of the population reject them completely.”