The journalists, who are charged with revealing state secrets, were arrested in November 2015 over a report alleging that the Turkish government had tried to ship arms to Islamists in Syria.
Can Dundar and Erdem Gul deny the charges but face possible life sentences if found guilty.
Their supporters say the case is a major test of press freedom in Turkey.
The Turkish government has come under increasing international criticism over its treatment of journalists.
Earlier this month, Turkish police raided the offices of the country’s biggest newspaper, Zaman, hours after a court ruling placed it under state control.
Over 100 reporters and observers attended the opening session of the trial on March 25.
Prosecutors then asked the judge for a closed hearing, a request which the judge approved, after a brief adjournment.
A Human Rights Watch observer present in the court called the decision “a travesty of justice”.
The adjournment came after more than a dozen opposition lawmakers refused to leave the courtroom. The judges filed a complaint against them for attempting to influence the trial.
Can Dundar, Cumhuriyet‘s editor-in-chief, and Erdem Gul, Ankara bureau chief, were arrested in November 2015.
President Recep Tayyip Erdogan personally filed a criminal complaint against the two journalists.
Can Dundar and Erdem Gul were held in pre-trial detention but were released in February after the Constitutional Court ruled their rights to liberty and free expression had been violated.
In a statement given just before the trial, Can Dundar said the government was trying to intimidate Turkey’s journalists.
“There is an effort to arrest an entire profession and the public – what foreigners call a <<chilling effect>>,” he said.
“What is trying to be created is a mechanism of self-censorship and an increasing empire of fear.”
Campaigners say the case is politically motivated and part of a growing crackdown on media critical of President Recep Tayyip Erdogan.
On March 24, dozens of prominent writers published an open letter to PM Ahmet Davutoglu, urging the government to drop the charges against the Cumhuriyet journalists.
“We believe that Can Dundar and Erdem Gul are facing life in prison simply for carrying out their legitimate work as journalists,” they said.
The letter also voiced concern over the “increasing climate of fear and censorship and the stifling of critical voices in Turkey”.
Zaman newspaper is closely linked to the Hizmet movement of influential US-based cleric Fethullah Gulen.
The government says Hizmet is a “terrorist” group aiming to overthrow President Erdogan.
Fethullah Gulen was once an ally of Recep Tayyip Erdogan but is now seen by the Turkish President as a threat to his authority.
According to the 2015 Reporters Without Borders’ World Press Freedom Index, Turkey ranks 149th amongst the 180 countries.
Media organizations in Turkey say that more than 30 journalists are currently behind bars and most are of Kurdish origin.
However, the government argues journalism in Turkey is among the most free in the world.
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