James Wood, 34, and Tanika Kristan Bromley, 33, were arrested in the Bundaberg area in southern Queensland late on Thursday, police said.
Pheobe was last seen near Bundaberg airport about 8.30am on May 15 after booking a trip to Western Australia to see her boyfriend.
CCTV footage indicated Pheobe never arrived at the airport terminal.
"The remains of Pheobe Bishop have not been located to date," a police statement said on Thursday night.
"Detectives continue to investigate this matter, and physical searches will continue as needed as information is provided."
Wood and Bromley have also been charged with two counts each of interfering with a corpse.
Wood had previously been taken into custody on Wednesday but was released several hours later without charge.
The search for Pheobe was scaled back on Wednesday after police had spent weeks combing several areas of interest in southern Queensland.
One of those areas was a property in Gin Gin where Pheobe had lived with Wood and Bromley.
The Gin Gin property near Bundaberg and a grey Hyundai ix35, thought to have been used to take Pheobe to the airport, were declared crime scenes soon after her disappearance.
The police search initially focused on Good Night Scrub national park, an hour's drive from Bundaberg airport, with homicide detectives, cadaver dogs and divers called in.
Some items believed to be linked to the investigation were seized for forensic examination.
The search revealed evidence might have been moved from the national park before police arrived.
Wood and Bromley had earlier been charged with unrelated weapons offences.
Pheobe's mum Kylie Johnson has been posting on social media almost every day pleading for information about her daughter's whereabouts.
Her latest update documented the heartbreaking toll the disappearance of Pheobe is having on the family.
"I don't know if life will ever be the same again? I don't know if I will ever look at the world the same way that I did before May 15th," Ms Johnson posted on Facebook on Wednesday.
"What I do know is that people have information on where you are Phee and we need that reported to police."
The community had rallied around the missing teen's family during the search with a "Leave the Lights On for Pheobe" campaign.
Gin Gin locals posted photos on social media of their front lights switched on "to guide Pheobe home".
Wood and Bromley are set to appear in Bundaberg Magistrates Court on Friday.
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