Mr Wilson decided to leave his role as director of business operations with the Royal Zoological Society of Scotland (RZSS) earlier this week, but the RZSS would not comment on the reasons for his exit.
It followed the news that Professor Chris West will be the next chief executive of the RZSS, having quit the same post in Adelaide, Australia, after six years at the helm.
Prof West, a former London Zoo director, will replace interim chief executive Hugh Roberts, who filled a leadership void last May amid a crisis that saw a director sacked and two suspended, including Mr Wilson, amid investigations into anonymous allegations. The same month, Donald Emslie resigned as chairman.
Mr Wilson, who was chief operating officer at the time, was suspended last March while inquiries were carried out by the board. He was subsequently cleared of all allegations.
Iain Valentine, the director of animals, conservation and education, was also suspended in April last year amid “very serious” allegations. Mr Valentine was cleared to return in what appeared to be a reduced role.
Reacting to the news that Mr Wilson had quit his business operations position, Jeremy Balfour, Conservative councillor for Corstorphine/Murrayfield, said: “What I am concerned about is that the zoo moves on from this now. Hopefully, the new management can bring a bit of stability.”
Paul Edie, Liberal Democrat councillor for Corstorphine/Murrayfield, said: “The zoo has had a rocky time. They have had a huge shot in the arm with the acquisition of the pandas and they have got a new chief executive. I look forward to working with them and moving forward into the future.”
A spokeswoman for the RZSS said: “Gary was responsible for on-site development projects, visitor services and the retail arm. We extend our thanks to him for all his work.”
Mr Wilson could not be contacted for comment.