Their trial is expected to last for at least three days.
Michael Kavanagh, 11 Ballybough, Greencastle a master of the Father McKee boat, pleaded not guilty to failing to make an accurate landing declaration of catch within 48 hours, on dates in September 2004 and October 2004.
His co-accused, Brendan Gill, The Cottage, Greencastle, captain of the Brendallon boat, also denied two counts of failing to make an accurate landing declaration of catch within 48 hours on two dates in September 2004.
Senior Counsel for the Attorney General, Thomas O'Connell told the court that the Prosecution was reducing the number of charges from eight to four.
He added that the defendants were arraigned on two charges each.
A jury was sworn in this morning, and the trial is expected to begin at 2pm today.
Judge Keenan Johnston said he was concerned about the number of potential jurors who failed to turn up.
He said he was asking the Court Registrar to write to those who did not attend. And if they failed to give a satisfactory explanation as to why they did not turn up, they could be summoned to the district court, where they could face a fine.