Since the end of apartheid the Khoisan have gained limited recognition and projects have been set-up to preserve indigenous culture.
Khoisan, previously called Hottentots and Bushmen, were dispossessed by the colonialists and oppressed by the apartheid regime, and now they say they are being marginalised in South Africa.
At a conference, which ended on Sunday, they argued for legal protection of their culture and language.
Since the end of apartheid the Khoisan have gained limited recognition and projects have been set-up to preserve indigenous culture.
South Africa's Deputy President Jacob Zuma said that he detected a growing sense of pride amongst the country's indigenous people.
He told delegates: "You have taken charge of your own heritage and your own destiny."
Mr Zuma also acknowledged the important role that the Khoisan have played in the country.
Assimilation
Approximately one million South Africans (2% of the population) are believed to have Khoisan origins. But many have assimilated.
Few people speak any of the indigenous languages or maintain a traditional lifestyle.
Delegates at the conference wanted the Khoisan identity to be recognised in the constitution and for their languages to be taught in schools.
They were also concerned about the issue of land restitution.
The existing law only applied to land seized after 1913. The Khoisan say that they were dispossessed long before that.
They are urging the government to look into land thefts dating back to 1652.