Forensic tests on two bodies found in the Colombian jungle show that they are those of Oscar Villains and Katty Velasco, an Ecuadorean couple kidnapped on 17 April.
The tests also suggest they were stabbed to death two months ago.
They had been kidnapped by dissident members of the now dissolved Colombian rebel group Farc.
The dissident gang is led by a man known as Guacho, who refused to follow the Farc's orders to lay down arms.
He broke away from the Farc and founded the Oliver Sinisterra Front, which is thought to have about 70 to 80 combatants.
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His gang has been active in the Ecuador-Colombia border area for the past two years.
Mr Villacís, 24, and Ms Velasco, 20, went missing from Puerto Rico, a rural area near the Colombian town of Tumaco, on the border with Ecuador.
Four days after their disappearance, the gang released a video of the two with ropes around their necks and their hands tied. They asked Ecuadorean President Lenín Moreno to give the kidnappers whatever they were asking for so that the two of them would be released.
The video, which was shown at a news conference by the Ecuadorean defence minister, shocked Ecuadoreans already enraged by the kidnapping and killing of two journalists and their driver by the same gang the previous month.
In the aftermath of the two kidnappings, Colombian and Ecuadorean forces launched a joint operation to capture Guacho but have so far failed to locate him in the thick jungle border area which is his stronghold.
The remains of the journalists and their driver were found last month. It took days to retrieve them because they had been booby trapped.
The bodies of Ms Velasco and Mr Villacís were found near Tumaco earlier this week.
Ms Velasco's sister travelled to the town, where the head of the forensic team, Carlos Valdés, confirmed her worst fears.
Mr Valdés said the couple had died "due to blood loss caused by sharp objects".
The Ecuadorean government said it would not rest until those responsible had been brought to justice.