Rebels from the Revolutionary Armed Forces of Colombia (Farc) have declared war on the smaller guerrilla group, the National Liberation Army (ELN).
The Farc and ELN have been at war with the state for decades
A statement posted on the Farc's website accuses the ELN of "attacks that we only expected from the enemy".
The flashpoint is in the province of Arauca, near the Venezuelan border, where the Farc have been trying to take over ELN sources of income.
Analysts say the conflict is likely to play into the hands of the government.
The BBC's Jeremy McDermott in Bogota says that although the Farc are supposedly allied with the ELN, in practice the groups have never worked closely together.
The Farc have for some years moved to take over ELN territory near the Venezuelan border, and the smaller rebel army reacted by killing several Farc militants.
The statement posted on the Farc website on Sunday comes from the Farc's "Eastern Bloc".
"From the ranks of the ELN we have received attacks that we only expected from the enemy," it said.
"We have tried on several occasions to give them the benefit of the doubt as fellow revolutionaries, but we have not received a response that helped to build fraternal relations, and for this reason have decided to punish those responsible."
The statement goes on to say that Farc had no desire to harm ordinary people but that the problem was with ELN commanders "who treat us as the enemy".
It calls on ELN guerrillas "to use their arms for the good of the revolution and not against their brothers in arms" - an implicit invitation for ELN members to defect.
There is nothing likely to make the Colombian army happier than the prospect of the two principal Marxist rebel groups fighting each other, our correspondent adds.
President Alvaro Uribe, since coming to power in 2002, has stepped up the war on left-wing rebels while saying he is open to negotiations.
The ELN is now in talks with the government to see if common ground for a lasting peace deal can be found.
Our correspondent says this declaration of war, although geographically restricted, may give the government the opportunity to remove the ELN from the conflict and concentrate its full military effort on the Farc.