Greg Lynn, 55, was arrested on Monday night after police helicopters descended on his campsite in Victoria.
He was charged with murdering Russell Hill, 74, and Carol Clay, 73. There has been no trace of the pair since March last year.
On Friday, Mr Lynn was remanded in custody to face a court next year.
He was stood down as a pilot by Jetstar - a budget airline owned by Qantas - shortly after his arrest.
The disappearance of Mr Hill and Ms Clay from the Victorian Alpine National Park sparked one of the state's largest missing person investigations.