The Master of the super-trawler, Gerrit Plug, 57, is accused of breaches of EU fishing regulations off Tory Island in November.
The trawler was previously known as the Atlantic Dawn when it operated out of Killybegs.
The vessel is free to continue fishing on €250,000 bail set by the High Court.
It is accused of discarding smaller fish in breach of EU regulations and failing to make the correct log-book entry.
The accusations allege the Master high-graded the catch by discarding smaller fish, known as horse-mackerel or scads, and retaining larger fish to increase the value of the catch.
Both prosecution and defence agreed to an adjournment to the next sitting of the Circuit Court in Donegal town on May.
The 144-metre, 14,000 tonne Annelies Ilena was detained at the time of the alleged offence by the Irish Naval Service.