Alexander Baird, 55, of Kirkcudbright, Dumfries and Galloway, went before Caernarfon Crown Court on Monday.
He has been charged with failing to take all reasonable steps to ensure the safe operation of a vessel.
In January 2012, a crewman on the scallop dredger, Steven Robertson, 25, of Dalbeattie, Dumfries and Galloway, was lost while aboard the St Amant.
The body of Mr Robertson was never found.
Mr Baird will appear in court again at the end of February.
A fishing boat master has appeared in court almost four years after a crewman was lost overboard off Anglesey.