By Jeremy McDermott
BBC News, Medellin
Reyes headed negotiations with ex-president Andres Pastrana's team
The death of Raul Reyes marks the first time a member of Farc's ruling body, the Secretariat, has been killed in combat during four decades of fighting.
"This is the greatest blow to Farc to date," said Colombian Defence Minister Juan Manuel Santos.
He was flanked by smiling commanders of the security forces at a press conference describing the operation that led to the death of Reyes, whose real name was Luis Edgar Devia.
The operation to kill Reyes began in the early hours of Saturday morning when the Colombian army received confirmation from a spy that the guerrilla commander was in a hamlet called Santa Rosa just across the border in Ecuador.
Planes were sent to bombard the camp, followed by troops in helicopters who recovered the bodies of Reyes and another 16 rebels.
Also among the dead was Guillermo Enrique Torres, alias Julian Conrado, a Farc commander known for his music, who had released several compilations of revolutionary ballads that he wrote and sang.
Colombian President Alvaro Uribe spoke to his Ecuadorean counterpart Rafael Correa informing him of the action.
The killing of Reyes has shattered the myth of invincibility that surrounded Farc's leadership.
The group's founder and leader, Manuel Marulanda, whose real name is Pedro Marin, is now in his 70s.
He has survived numerous attempts on his life and previous members of the Secretariat have all died of natural causes.
"This heralds the final phase of the war," said retired General Harold Bedoya, a former head of the armed forces.
What the operation shows is that the intelligence wing of Colombia's security forces has managed to penetrate even the close circles of Secretariat members.
The government has set up a network of informants, runs reinsertion packages for deserting rebels and offers handsome rewards for information.
In the past few days, almost $900,000 was paid for the capture of a Farc commander with 35 years of service.
During interviews, Reyes was unfailingly polite and unswervingly orthodox in his Marxist Leninism
All this is combined with technology and communication intercepts provided by Washington.
Roman Ortiz, an analyst with the Bogota think tank Ideas for Peace Foundation, believes this is a blow Farc will have difficulty recovering from.
"This is a definitive blow to the guerrillas and one which will seriously affect their cohesion as an organisation," he said.
The death of Reyes will hurt Farc diplomatically as he was the head of the International Front, the part of the guerrilla movement dedicated to developing foreign contacts and links with like-minded organisations.
During the failed peace process with former president Andres Pastrana which ran from 1998-2002, Reyes headed Farc's negotiating team, based in Los Pozos, a dusty hamlet in the 42,000 sq km safe haven that the government granted to the guerrillas as the venue for talks.
Cold War rhetoric
A squat figure, Reyes was held both in affection and a little awe by the rank and file guerrillas.
He was the public face of Farc, baffling both national and international journalists with a discourse straight out of the Cold War, by then just a memory.
During the innumerable interviews I had with him he never deviated from the party line, was unfailingly polite and unswervingly orthodox in his Marxist Leninism.
Reyes also played a pivotal role in the issue of hostage releases.
It was he that met with Colombian senator Peidad Cordoba, who has been working with President Hugo Chavez of Venezuela, securing the release of six of the 40-odd political hostages in Farc hands.
The guerrillas want to exchange the remainder of their prisoners for hundreds of rebels in Colombian jails.
Farc has said it will not release any more hostages until the government grants it a demilitarised zone to negotiate, something President Uribe has ruled out.
While unprecedented in its scale, this is not the first time a Farc commander has been killed in a military operation, with an infiltrator pinpointing a location and the Colombian air force dropping massive amounts of ordnance on the site.
In a grave blow to Farc finances the head of the 16th Front, Tomas Medina, alias Negro Acacio was killed last September in a similar operation, this time in the province of Vichada, by the Venezuelan border.
He was one of Farc's drug lords, handling the exportation of cocaine, one of the main sources of revenue for the guerrillas.