BOSTON — For the first time in at least a century, U.S. fishermen won’t take too much of any species from the sea, one of the nation’s top fishery scientists says.

The projected end of overfishing comes during a turbulent fishing year that’s seen New England fishermen switch to a radically new management system. But scientist Steve Murawski said that for the first time in written fishing history, which goes back to 1900, "As far as we know, we’ve hit the right levels, which is a milestone."

"And this isn’t just a decadal milestone, this is a century phenomenon," said Murawski, who retired last week as chief scientist at the National Oceanic and Atmospheric Administration’s Fisheries Service.

Murawski said it’s more than a dramatic benchmark — it also signals the coming of increasingly healthy stocks and better days for fishermen who’ve suffered financially. In New England, the fleet has deteriorated since the mid-1990s from 1,200 boats to only about 580, but Murawski believes fishermen may have already endured their worst times.

"I honestly think that’s true, and that’s why I think it’s a newsworthy event," said Murawski, now a professor at the University of South Florida.

But fishermen and their advocates say ending overfishing came at an unnecessarily high cost. Dave Marciano fished out of Gloucester, an hour’s drive northeast of Boston, for three decades until he was forced to sell his fishing permit in June. He said the new system made it too costly to catch enough fish to stay in business.

"It ruined me," said Marciano, 45. "We could have ended overfishing and had a lot more consideration for the human side of the fishery."

An end to overfishing doesn’t mean all stocks are healthy, but scientists believe it’s a crucial step to getting there.

When fishermen are overfishing a species, they’re catching it at a rate scientists believe is too fast to ensure that the species can rebuild and then stay healthy. It’s different from when a species is overfished, which is when scientists believe its population is too low.

Murawski said it’s a nearly ironclad rule of fishery management that species become far more abundant when they’re being fished at the appropriate level, which is determined after considering factors such as a species’ life span and death rates.

A mandate to end overfishing by the 2010 fishing year — which concludes at different times in 2011, depending on the region — came in the 2007 reauthorization of the nation’s fisheries law, the Magnuson-Stevens Act.

Murawski said the U.S. is the only country that has a law that defines overfishing and requires its fishermen not to engage in it.

"When you compare the United States with the European Union, with Asian countries, et cetera, we are the only industrialized fishing nation who actually has succeeded in ending overfishing," he said.

Regulators say 37 stocks nationwide last year were being overfished (counting only those that live exclusively in U.S. waters); New England had the most with 10. But Murawski said management systems that emphasize strict catch limits have made a big difference, and New England just made the switch.

Fishermen there now work in groups called sectors to divide an annual quota of groundfish, which include cod, haddock and flounder. If they exceed their limits on one species, they’re forced to stop fishing on all species.

About two-thirds into the current fishing year, which ends April 30, federal data indicated New England fishermen were on pace to catch fewer than their allotted fish in all but one stock, Georges Bank winter flounder. But Murawski said he didn’t expect fishermen would exceed their quota on any stock.

In other regions with overfishing — the South Atlantic, the Gulf of Mexico and the Caribbean — regulators project catch limits and other measures will end overfishing this fishing year. Already, South Atlantic black grouper and Gulf of Mexico red snapper are no longer being overfished.

The final verification that overfishing has ended nationwide, at least for one fishing year, will come after detailed stock assessments.

It will be a "Pyrrhic victory" in hard-hit New England, said Brian Rothschild, a fisheries scientist at the University of Massachusetts at Dartmouth. He said regulators could legally loosen the rules and allow fishermen to safely catch more fish, but regulators have refused to do it, and fishermen have needlessly been shut out from even healthy stocks.

The science is far from perfect, Marciano said. Regulators believed fishermen were overfishing pollock until new data last year indicated scientists had badly underestimated its population, he said. And some stocks, such as Gulf of Maine cod, have recovered even when fishermen were technically overfishing them.

"To say you can’t rebuild stocks while overfishing is occurring is an outright lie. We did it," Marciano said.

Tom Nies, a fisheries analyst for regional New England regulators, said stocks can sometimes be boosted by variables such as strong births in a given year, but they’ll inevitably decline if overfishing continues on them.

Peter Shelley, senior counsel of the Conservation Law Foundation, an environmental group, said the industry’s problems are rooted in years of overfishing, especially during the 1980s, not regulation.

"It was a bubble," he said. "Fishermen were living in a bit of a fantasy world at that point, and it wasn’t something you could sustain."

That’s why Murawski’s projection about the end of overfishing is "a very big deal," he said.

"I think we’re just starting to see signs of a new future," Shelley said.

What fisherman Steve Arnold, 46, sees in his home port of Point Judith, R.I., are fewer boats, older fishermen and "a lot of frowns on people’s faces."

Overfishing might end this year, but the fleet has suffered and has an uncertain future, he said.

"I believe we can get to a better place, but the work isn’t done," Arnold said. "We’re living through something that we’re learning as we go. It’s not a comfortable feeling."