Mr Neil Evers, a direct descendant of the Garigal clan of Guringai language people, unveiled the plaque with the Commanding Officer Penguin Commander Paul Gall.
At the unveiling, Mr Evers paid his respects to the elders of the Camergal clan, whose Country the base stands on.
Mayor of Mosman, Peter Abelson, traditional elders and descendants of Bungaree - the leader of the Garigal clan, attended the unveiling, which included a smoking ceremony, a didgeridoo player and Penguin’s ship’s company.
In his address, Commander Gall said the Navy had long recognised links with the first Australians.
“The Royal Australian Navy has a proud history of engagement with Indigenous Australians.
“King Bungaree was of the Garigal clan from Broken Bay and was the first Australian born circumnavigator of our country.
“He rounded the continent with Matthew Flinders in the sloop HMS Investigator during 1802-03.”
Later, Governor Macquarie asked him to be in charge of a farming community comprising of 16 Aboriginal families located on Middle Head.
“We are lucky to have here today, two relatives of Bungaree, Mr Laurie Bimson and Mr Neil Evers,” Commander Gall said.
“Today we recognise the traditional owners of the land, the contribution made by indigenous men and women who have contributed to the Defence of Australia in times of peace and war.
“We also take the time to celebrate the diversity of the Navy’s workforce.”
Mr Evers said his ancestors would be pleased by the recognition.
“Our ancestors would be so happy to see what is happening here today, on the behalf of them I would like to thank all those involved with this event.
“It’s with your help the first people of this nation are being recognised,” Mr Evers said.
Just over 1.5% of Navy’s workforce identify as Indigenous, a figure which Commander Gall says Navy is actively trying to increase through active recruitment.
“I am proud to work in an organisation that is inclusive and committed to increasing the number of indigenous people serving at sea and ashore.”
Navy runs a Defence Indigenous Development Program and is a strong supporter of the Indigenous Pre Recruitment course, a six week program run in conjunction with TAFE.
“Demonstrating that Navy has come a long way in recognising its indigenous personnel, in 2013 Navy formed an Indigenous Performance Group, ‘Bungaree’, made up of currently serving, full time members, who share their culture through traditional dance,” Commander Gall said.