Journalist and commentator Mehmet Altan, 65, was in January ordered to be freed by the Constitutional Court but its ruling was not implemented by the criminal court in a move that outraged supporters.
Still under arrest, Altan went on trial with six others including his brother Ahmet Altan, 67, and the veteran journalist Nazli Ilicak, 73.
They are charged with links to the group of US-based preacher Fethullah Gulen blamed for the 2016 failed coup and face life in jail if convicted. They all deny the charges.
The failure to release Mehmet Altan and fellow writer Sahin Alpay -- who is being tried in a separate case -- raised new alarm over the rule of law in Turkey.
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The Altan brothers have been held in jail since September 2016.
The Ankara-based Constitutional Court had ruled that Mehmet Altan and Alpay should be freed on the grounds that their rights had been violated.
But the Istanbul criminal court refused to implement the order, saying it had not been properly communicated in a move that raised fears of political interference.
Dozens of Turkish journalists have been arrested in the crackdown that followed the coup in what critics have slammed as a major erosion of freedom of speech.
"It is the freedom of thought that is on trial; this is the conclusion of the Constitutional Court decision as well," the defence lawyers said in a joint statement published by P24.
"We expect an end to the severe, grave juridical fallacy embodied in the case," they added.