Police identified the remains found by a hilllwaker on Salisbury Crags on March 9 as belonging to Alan Templeton, who was last seen in November 2006.
It is understood that DNA samples were used to identify Mr Templeton, and officers said that “no suspicious circumstances” surrounded his death.
The remains are thought to have lain in the spot ever since the 25-year-old was first reported missing.
His older sister, Kirsten, who lives in Paris, broke the news of his death to supporters on the Facebook page set up to help track down Mr Templeton.
She said: “Alan has sadly been found dead in Edinburgh. His identity has now been confirmed by police.
“We would like to thank all of you for all the support you have brought us over the last five and a half years, thank you for being Alan’s friends and for caring.”
Mr Templeton, who had been working at the Halo bar in Melville Place, had not been seen since leaving a friend’s flat on November 26, 2006.
A former police officer, who worked on a number of missing person cases, told the Evening News he was not surprised that Mr Templeton’s body had gone undiscovered for so long.
He said: “The spot where the remains were recovered is a very severe slope where walkers and dogs are not going to reach easily. If the police never searched that area while looking for him it’s difficult to see how it would be found. Even if they had searched there it would be possible to miss.
“Bodies can be amazingly difficult to detect.”
The discovery of Mr Templeton is the second time in recent years that remains have been found in Holyrood Park.
Seven months before Mr Templeton disappeared, police confirmed that remains found near Duddingtson Loch belonged to a homeless man who went missing in August 2005.
The disappearance of father-of-two William Young, 29, from Edinburgh, was never reported to police.
He was identified through DNA taken from the skeletal remains found in wet marshland by Historic Scotland staff in March 2006.
Police said that a report would now be sent to the procurator fiscal over Mr Templeton’s death. His funeral will be held at Canongate Kirk at 2pm on Friday followed by Warriston Crematorium at 4pm.
He was suffering from depression and disappeared only a month after returning to the Capital, where he was living with a friend in Newington, following two years living in Paris.
Along with his older sister and younger brother Calum, Mr Templeton was brought up in Stockbridge. After graduating from the University of Wales with dreams of becoming a documentary filmmaker or a photographer, he moved to Paris in search of work.
Just weeks before his remains were found in Holyrood Park, his mother, Elizabeth, talked about her experiences on ArtWorks Scotland: The Missing, a documentary dealing with the impact of the sudden disappearance of a loved one.
Search continues for Mary
OF the remaining missing person cases in the Lothians, the search for pensioner Mary Ferns remains one of the highest profile.
The 88-year-old vanished during a shopping trip that took her from her Livingston home to Edinburgh.
Mrs Ferns was spotted on CCTV as she made her way eastwards along Princes Street and past the Balmoral Hotel on June 17, 2008.
Fears grew for Mrs Ferns after human remains were discovered on the banks of the River Almond in Livingston in April last year, but inquiries established in February that the remains were of 56-year-old James Adams, who vanished in 1996.
Search teams discovered his remains while looking for Mrs Ferns, and initially thought it may have been her.
She is described as being white, around 5ft 3in tall, of slim build, with short grey hair and green eyes.