Michel Gbagbo, who has dual French and Ivorian nationality, was charged along with other close allies of his father.
They include the former prime minister and head of Mr Gbagbo’s Ivorian Popular Front (PFI), Pascal Affi N’Guessan.
The group was among dozens put under house arrest with Mr Gbagbo in April.
The BBC’s John James in Abidjan says all the key figures arrested with Mr Gbagbo have now been charged, except for the former president and his wife Simone.
They are being held in separate towns in the north – a stronghold of President Alassane Ouattara – and could be investigated by the International Criminal Court, our reporter says.
The 12 are charged with taking part in an armed insurrection and attempting to undermine the state in the world’s largest cocoa producer.
Human rights groups strongly condemned their four-month detention, calling for them to be charged or released.
Mr Ouattara has always insisted that those on both sides of the political divide would face justice if they committed crimes during the five-month dispute.
So far, none of his supporters have been arrested or charged, even though human rights groups have accused some of them of killing people suspected of backing Mr Gbagbo.