Michael Stimson's vessel Alicia was detained as "dangerously unsafe" after it was boarded by Fisheries Officers in October 2013.
Stimson was jailed for four months at a hearing at Southampton Crown Court.
David Fuller, of the Maritime and Coastguard Agency (MCA), said full compliance with safety was essential.
The MCA said Stimson turned off his navigation lights when approached by a fisheries patrol vessel when he had been seen in an area closed to fishing because of E-coli concerns.
Investigations showed the boat was unstable and the two crewmen on board had received no safety training.
Stimson, 32, of Ladycross Road, Southampton, had pleaded guilty to three offences brought under Maritime safety legislation and two under food safety and hygiene regulations.
The skipper of a fishing vessel who admitted maritime safety offences after operating in a closed area of Southampton Water, has been jailed.