Police declined to say how the two had died, saying that they would wait for the autopsy to confirm their identities and cause of death.
The bodies were discovered on a highway in northern British Columbia, 12 miles from Liard Hot Springs.
Police deployed tracker dogs, a drone and search planes to comb the hard, forested and swampy terrain, which was infested with mosquitos and home to bears and wolves.
An American, Chynna Deese, and her Australian boyfriend, Lucas Fowler, were found dead with gunshot wounds on the side of a highway July 15 in British Columbia.
Bryer Schmegelsky and Kam MacLeod have sent Canadian law enforcement on a trying chase through rough terrain for weeks now.
Mounties in Manitoba have confirmed two bodies believed to belong to the two murder suspects from Port Alberni were found approximately eight kilometres from where a burned SUV was found last month near the small community of Gillam.
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However, an underwater recovery team searched the river outside Gillam and found no "additional items linked to the suspects", a release said.
"It's a dense place, very hard to find anybody, really", MacLatchy said.
They say the bodies were found within a kilometre from those items.
On 23 July the search was refocused on Manitoba, after the a burnt-out vehicle reportedly used by the pair was found near Gillam. Authorities charged the teens with second degree murder in his death.
MacLatchy said officers searching the area on foot discovered the bodies.
"They're not going to give us false information and I appreciate that", he said.
She thanked all Canadians for remaining vigilant, particularly the communities of Gillam, Fox Lake Cree Nation, Ilford War Lake First Nation and York Landing in northern Manitoba.