The study's findings show there is a high level of genetic variety among Aboriginal Australians.
Aboriginal elder Lesley Williams, who was an adviser to the study, says Aboriginal people are increasingly interested in their genetic history.
"I'm not surprised, but still heartened, to discover that this DNA analysis supports what our parents have taught us over many generations - that we have lived here in Australia since the Dreamtime."
Nano Nagle, one of the study's authors, told AAP the results suggest “there's more than a single group, and at least two routes of entry."
Previous studies have found Aboriginal Australians arrived in Australia up to 55,000 years ago via the Indonesian island chain. But there has been ongoing debate among archaeologists, anthropologists and scientists about when they arrived, and the path they took to get here.
"Our findings confirm they were isolated in Australia for tens of thousands of years before European colonisation," Ms Nagle said.
"It confirms what Indigenous people have passed on from generation to generation."
Ms Nagle said the findings, which were published in the Journal of Human Genetics, represents between five and six years of research.
Previous mitochondrial DNA studies on Aboriginal Australians have involved fewer than 100 participants.
Despite being one of the oldest continuous cultures in the world, Aboriginal Australians are one of the most poorly studied populations from a human evolution perspective, Ms Nagle says.