Brendan Breen, 55, the brother of St Kilda football champion Barry Breen, was last seen at the Hilton Hotel at Melbourne's South Wharf on April 12, 2012.
He was reported missing on May 9 by his former spouse, who became concerned when Mr Breen cancelled dinner with her in a last-minute text message and then stopped answering her calls.
Investigators initially believed Mr Breen had chosen to disappear of his own accord, but a recent review of the case caused detectives to believe he may have met with foul play.
Brian James Hall, 72, was arrested at his home in Colac, west of Geelong, on Friday morning and later charged with one count of murder.
He faced Melbourne Magistrates Court on Friday afternoon for a brief hearing.
Hall was remanded in custody to next face court for a committal mention via video link on July 17.
The murder charge followed police arresting and releasing a 42-year-old Brisbane man without charge in March, after an earlier appeal for information on Mr Breen's disappearance.
Mr Breen was known to police and had previously been charged with fraud offences, spending several years behind bars.
He went by several other names, including Brendan Green, Brian Greer and Brendan Lacombe.
His twin sister, Fiona, made an emotional plea for information on behalf of the family in February.
Over the past 14 years, police said they spoke to Mr Breen's friends and associates in an effort to find him.
Detective Inspector Dave Dunstan said several aspects of the case gave investigators cause for concern, especially the period of time Mr Breen had been missing "with no trace whatsoever".
"We know he had a number of associates who were also known to police and, while they have been spoken to over the years, this remains an active avenue of inquiry for investigators," he told reporters in February.
Mr Breen failed to attend his daughter's wedding about a month after he disappeared in 2012 and missed her funeral in 2018.
Police previously revealed his bank accounts and phone had never been accessed, with no reported sightings of him in the years since.
Mr Breen's brother Barry played 300 games for St Kilda in the VFL between the mid-1960s to 1980s.
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