The Venezualen leader has been trying to broker an exchange of hostages for imprisoned Farc members.
Marulanda has not been seen or heard from in years and there has been suggestions that the Farc leader had died. If he is alive, he would be 79 years old.
"For years no one has known whether he is alive or dead," said Mariana Sanchez, Al Jazeera's South America correspondent.
She said that the letter would mean "Farc is sending a message not only to Hugo Chavez but to Colombia's goververment that it is willing to negotiate at the highest level".
Chavez, who did not reveal all of the letter's contents, said that Marulanda "still can't come to Venezuela" but was inviting him "to go to Colombia".
"It's difficult for me to go into the jungles of Colombia," he said. "But we're moving along."
Among about 45 prominent hostages held by Farc are three US defence contractors and Ingrid Betancourt, a French-Colombian citizen and former presidential candidate.
Chavez has called Colombia's long-running conflict an "important obstacle" to regional integration, but has said he will attempt to resolve it.
"If I have to go to the gates of hell to try for a humanitarian accord - and beyond that a peace accord in the beloved sister nation of Colombia - well I will go there with your approval," Chavez told supporters during a speech in Caracas, the Venezuelan capital.
For years the Colombian government and Farc have voiced support in principle for an exchange of hostages for prisoners but have never agreed on how to achieve it.