Brendan Breen, 55, the brother of St Kilda legend Barry Breen, was last seen at the Hilton Hotel at Melbourne's South Wharf in April 2012.
Mr Breen's former spouse reported him missing a month later after becoming concerned when he cancelled dinner plans in a last-minute text message and then stopped answering her calls.
Investigators initially thought he had chosen to disappear of his own accord but, following a case review, believe he met with foul play.
Brian James Hall, 72, appeared before the Melbourne Magistrates Court via videolink from custody on Friday where he pleaded not guilty to one count of murder.
Hall is alleged to have murdered Mr Breen in Toorak, in Melbourne's inner east, between April 11 and 13, 2012.
His case will return to the Supreme Court for a directions hearing on August 6.
Police arrested and then released a 42-year-old Brisbane man without charge in March, after an earlier appeal for information on Mr Breen's disappearance.
The victim - who also went by Brendan Green, Brian Greer and Brendan Lacombe - was known to police and had previously been charged with fraud offences, spending several years behind bars.
His twin sister, Fiona, made an emotional plea for information in February, saying she had an inkling something was not right.
"It's very hard. How can you explain how you feel when you don't know what's happened to him?" she said.
She said her fears were cemented when Mr Breen failed to attend his daughter's wedding about a month after he disappeared and missed her funeral in 2018.
His bank accounts and phone had never been accessed, with no reported sightings of him in the years since his disappearance, police said.
They had spoken to Mr Breen's friends and associates over the past 14 years 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 he had been missing "with no trace whatsoever".
Mr Breen's brother Barry is a St Kilda legend, playing 300 games in the red, black and white, including in the 1966 premiership team when his last-quarter point edged the Saints ahead of powerhouse Collingwood.
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