The 2,400-page indictment naming publisher Ragip Zarakolu and Professor Busra Ersanli resulted from an investigation of the Kurdistan Communities Union, or KCK, Today's Zaman reported.
The KCK is reportedly an umbrella group encompassing the terrorist Kurdistan Workers Party and its affiliated organizations that seek an autonomous Kurdistan.
Both men were arrested in November.
The indictment charges Ersanli with teaching a training course for the Peace and Democracy Party that was heavily influenced by the Kurdistan Workers Party and the KCK.
The prosecution said it considers Ersanli as leader of the group since he was in charge of the training program.
Zarakolu is accused of aiding the group.
The two face lengthy prison sentences if convicted.