Alan Morison and his Thai colleague Chutima Sidasathien appeared in a criminal court in the southern island of Phuket to hear charges of defamation and violation of the 2007 Computer Crime Act.
The duo could face up to seven years in prison and a fine of 100,000 baht (USD 3,010) if found guilty.
The charges relate to an article posted on the English- language news website Phuketwan last July carrying excerpts from a report by an international news agency alleging that some members of the Thai military were involved in trafficking captured illegal immigrants from Myanmar's Rohingya ethnic minority.
Both defendants were released on 100,000 baht bail.
The news agency has not been charged over its reporting.
The charges against the journalists came several days after the news agency won a Pulitzer Prize in international reporting for its series on the violent persecution of the Rohingya.