Sener and Sık, journalists arrested in March and held since in a top-security prison outside İstanbul, were among 14 defendants in court to open their defence on Thursday.
Sık and Sener are accused of belonging to Ergenekon, an ultra-nationalist group accused by prosecutors of being behind multiple conspiracies against Prime Minister Recep Tayyip Erdogan's Justice and Development Party (AK Party) government.
If found guilty the two face a maximum of 15 years in prison. Both have denied the charges and say the evidence against them was planted.
Investigations into Ergenekon have spiralled since they first opened in 2007, and critics accuse the government of scaremongering to silence opponents. The government denies any such motives.
Several hundred suspects, including retired senior military officers, academics, lawyers and journalists have been detained in cases related to Ergenekon.
The other defendants in court on Thursday included Yalcın Kucuk, an author and television debate show presenter, and Soner Yalcın, controversial editor of Oda TV, and several colleagues from the television website known for its criticism of the government.
Government officials say the journalists are on trial for criminal activities, not because of what they wrote.