South West fishermen face a £1m loss in business after a cut of 15% in the amount of Dover sole they can catch next year.
Fishermen in the region feared a 25% cut in cod catches
Fishermen say that will mean an 80 tonne cut in landings by boats at Plymouth and Brixham.
EU quotas agreed in Brussels will also mean an 8% cut in cod catches in the English Channel.
Fishing organisations say they are hopeful that quotas will be increased at negotiations for 2009.
There are increases for sole, hake and plaice in north Cornwall next year while quotas stay the same for same for monkfish, megrim, pollack, haddock and sole in the Western Approaches.
Fishermen said the cod cut was not as bad as the 25% feared.
Jim Portus, of the South West Fish Producer Organisation, said: "It's an unwelcome situation to be losing quotas, but over the next 12 months we should be looking at quotas going up as stocks are replenished.
"I remain optimistic that we shall get the quotas that fishermen so richly deserve."
UK Fisheries Minister Jonathan Shaw said a "fair settlement" had been reached on 2008 EU fishing quotas at the annual talks in Brussels.
A fifth of the South West fishing fleet, or eight boats, have been decommissioned over the past year at a cost of about £5m amid restrictions on when and where boats and operate.