Lewis Peter Carr (29) and Artur Sevash-Zade (34) appeared in the Royal Court on Friday.
Both denied unlawfully killing skipper Michael Michieli as well as crew members Jervis Baligat and Larry Simyunn.
The three men died when their fishing vessel L’Ecume II collided with Condor’s Commodore Goodwill freight ship on 8 December 2022.
Mr Carr was represented by Advocate Simon Thomas and Mr Sevash-Zade was represented by Advocate Mike Preston.
Crown Advocate Matthew Maletroit was prosecuting.
Mr Carr and Mr Sevash-Zade are on conditional bail and are due to return to court on 15 November, when a trial date will be set.