The joint flag-raising was the first time the two flags have flown together on the bridge, The Sydney Morning Herald reported. The flag-raising was accompanied by the Creation Stick Procession, a musical work depicting the aboriginal creation story.
"I'm pleased to be here today to witness an historic event, the raising of two flags on Australia Day," Charles Madden, an aboriginal elder who sits on the Aboriginal Land Council, said.
Some aboriginal Australians refer to Australia Day as Invasion Day.
Australia Day is the anniversary of the landing of the First Fleet in Sydney Cove on Jan. 26, 1788.
Around the country, thousands of people became citizens. They included Miriam Margolyes, the 71-year-old British-born actress best known recently as Professor Sprout in two Harry Potter movies, The Canberra Times reported.
Prime Minister Julia Gillard greeted Margolyes and other new citizens who participated in a ceremony in Canberra. Margolyes has lived in Australia part time since the 1980s. She told The Canberra Times in an interview she met her partner, an Australian woman, in London in 1968 and did not visit Australia until 1980.
She said she plans to keep her British citizenship as well.
''I am not the sort of person who divests myself of everything that came before I came to Australia," she said. "I want to take all the knowledge and experiences I gained when I was in England and put it at the service of Australia, because I have to bring something to Australia, not just money but myself."
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