PORTLAND – New England fishermen lost more days at sea effective Monday as new commercial fishing rules went into effect with the start of a new season.

Fishermen began operating under emergency rules issued by the National Marine Fisheries Service that further reduce days at sea and set stricter catch limits on certain species in an effort to rebuild depleted stocks of cod and yellowtail flounder in New England waters.

Overall, fishermen will lose another 8 percent of the number of days they’re allowed to fish, but there will be differences for large and small boats.

The latest restrictions follow a trend dating to 1996, when days at sea were cut to 196. Further cuts reduced the number to 88 in 1999, 70 in 2002, and 58 in 2004.

The latest rules were emergency measures implemented by the National Marine Fisheries Service. They will remain in effect until permanent rules recently passed by the New England Fishery Management Council are implemented later this year.

Barbara Stevenson, a boat owner in Portland, said she talked to her captain on Monday about what the changes would mean.

“Even though I explained it several times to my captain, he still didn’t understand what I’m saying. I can’t blame him,” she said.

Craig Pendleton, a Saco boat owner and coordinating director of the Northwest Atlantic Marine Alliance, said fishermen were still sorting out the rules and trying to map out strategy for taking advantage of the days that are available.

The emergency rules go into effect after a difficult April for many fishermen. Pendleton’s 54-foot boat just returned from a little more than three days at sea; the boat arrived in port with only 4,000 pounds of fish.

For all of the pain endured by fishermen, there’s little to show for the conservation measures, Pendleton said.

“We’ve faced all of these regulations for the last 10 years, and no one can look you in the eye and tell you things are better,” he said.