Jetstar pilot Greg Lynn has been charged with two counts of murder after spending several days being questioned by police over the disappearance of campers of Russell Hill and Carol Clay.
Victoria Police Crime Command Assistant Commissioner Bob Hill said Mr Lynn would appear in the Sale Magistrates' Court on Friday morning.
"We are hoping this arrest brings us a step closer to providing the answers the families have been desperately seeking and richly deserve," he said.
The couple were last heard from on March 20, 2020, from their remote Wonnangatta Valley campsite in the Victorian high country.
The campsite was later found burnt out, but Mr Hill's four-wheel drive was still there.
Assistant Commissioner Hill said police had established by mid-2020 that it was unlikely that the missing couple were alive.
On Monday night, special operations officers descended on a campsite near Moroka Road at Arbuckle Junction, roughly 55 kilometres south of the Wonnangatta Valley.
The officers arrested the 55-year-old from Caroline Springs in Melbourne's west and seized his Nissan Patrol for forensic testing.
'Extraordinary' investigation led to the arrest, police say
Assistant Commissioner Hill said police had been combing the Victorian countryside for the past 20 months for human remains or any clues that would provide answers to the mystery.
He said that, during the "extraordinary" investigation, police interviewed numerous people, inspected vehicles, analysed data and adopted "unique investigative techniques".
However, he said, the investigation was far from over.
"Our efforts to locate the remains of Russell and Carol will continue," Assistant Commissioner Hill said.
He said detectives identified a crime scene on Thursday morning within the Great Alpine area and forensic specialists would start searching at the location in the coming days.
But Assistant Commissioner Hill declined to reveal the exact location.
"Police are hopeful that we will be able to locate the deceased and provide ultimate closure to the families," he said.
"My heartfelt thoughts are with both the Hill and Clay families. The past 20 months have been an incredibly difficult time for them and I know their grief remains as raw as ever."
Assistant Commissioner Hill said police were "indebted" to the media and the community for their support, which had played a part in the investigations.
Police not looking for more suspects
He said police were keen to speak to anyone who was in the Wonnangatta area around the time of the couple's disappearance, including campers, day-trippers, hunters, fishermen or trail-bike riders, regardless of whether they saw or heard anything.
"We are also continuing to appeal to anyone who knows the whereabouts of a blue-coloured trailer that was attached to the Nissan Patrol to come forward," Assistant Commissioner Hill said.
"Police are keen to speak to anyone who purchased or received a similar trailer, particularly during the period of March and July last year.
"We believe the trailer was sold on [online market] Gumtree."
Police said the 7x5 trailer was a rusty silver/blue, with off-road wheels.
Assistant Commissioner Hill said no other person was being sought in connection with the investigation.
Anyone with information should contact CrimeStoppers on 1800 333 000.
