Before he heads out to sea, commercial fisherman Raymond Lees stops by Reidar’s Trawl Gear & Marine Supply in New Bedford to buy custom-designed fishing nets.

The shape of the net, the width of its mouth and the size of its holes all help him target certain species of fish and, perhaps more importantly, avoid others.

“I've spent so long running away from codfish that I've gotten better at running away from codfish,” Lees said during a recent run to Reidar’s. “I have specialized gear and I'm good at what I do.”

Avoiding cod, a popular choice for everything from fish and chips to chowder, is a strategy that flies in the face of New England’s long fishing tradition. Codfish, once the bedrock of the region’s fishing economy, is now subject to strict fishing quotas the federal government sets to help the species rebuild. For a generation of fishermen like Lees, cod has been known as a “choke species,” meaning fishermen sometimes catch so much of it, they hit their allotted quota and have to stop fishing for anything else.

“I've been scalloping for close to five years because I haven't been able to fish what I was traditionally trained to do,” Lees said, ”and that's chase codfish and flounders.”

Lees buys his nets from Tor Bendiksen, the owner of Reidar’s and a former fisherman himself. As Bendiksen trimmed a net design he and his father have been refining for decades, he said that New Bedford’s once-mighty groundfish fleet has been whittled down into a “mere nothing” because targeting cod is no longer economically viable for most fishermen.

“We went from a huge fishing business, as far as the groundfishing fleet’s concerned, of 300 boats down to 20 boats,” Bendiksen said. “It’s pretty much a 90 percent loss of what the fleet was.”

Fishing ports up and down the East Coast have suffered similar fates. It’s been a long fall for a fish foundational to the region’s economy. The fishery’s profits once lured the Pilgrims to Plymouth, and built a class of New England merchants who sparked a revolution to access international markets. The codfish went on to draw generations of immigrants from Portugal, Italy, Norway and Iceland to the region.

But after centuries of good catches, nets started to come up light in the 1980s. The federal government responded with the Magnuson-Stevens Act, a piece of legislation that kicked foreign fleets out of American fishing grounds. By 1994, the law was being used to close off areas of the ocean to American fishermen as well.

Some of those areas remain closed, and many regulators say that’s for good reason: they believe cod never rebounded the way they hoped it would.

But new research under review this year is challenging that claim.

“For the first time in about 20 years we've seen and are tracking a successful year class of cod, and they seem to be growing at a very good rate,” said Kevin Stokesbury, a fisheries science professor at UMass Dartmouth leading a multi-year survey of codfish in the Gulf of Maine.

Stokesbury’s survey is built around a new method for counting cod, which uses a GoPro camera mounted inside an open-ended fishing net to capture video of the cod passing through. The approach allows Stokesbury to survey for longer periods of time than a traditional government survey, which catches cod in a close-ended net and hauls them onboard for hand counting.

Stokesbury and his team have been following a healthy population of young cod in the Gulf of Maine for two years now. The “class of ‘19,” which Stokesbury named for the year it hatched, includes at least a million young codfish, according to his data – an unusually bountiful class that federal scientists say is not showing up in their surveys yet.

With three or four more classes like it, Stokesbury said the cod fishery could be back in business, similar to the way haddock, a close relative of cod, recovered 15 years ago.

“Haddock are quite similar to cod when you look at them,” Stokesbury said. “It is very possible that you could have a rebound.”

Stokesbury has a history of using scientific innovation to produce new findings that upend fishing regulations. In the 1990s, he devised a new way of counting scallops that helped open up a tightly regulated fishery.

A typical government-led survey determines scallop numbers by dredging the ocean floor, counting the scallops it pulls up, and estimating what percentage that is of the total scallops in the sample area. Stokesbury’s surveys rely on pictures of the ocean floor instead. A team of his undergraduates count all the scallops in their sample areas one-by-one, eliminating much of the guesswork.

Stokesbury’s method for counting scallops was peer reviewed and eventually incorporated into the government’s periodic stock assessments, which form the basis of fishing regulations in America. In the early 2000s, regulators had already suspected scallops were rebounding to some extent, but Stokesbury’s findings upended what they had been saying for years.

“They thought there were two to three times as many scallops in there,” Stokesbury said, “and there were actually about 14 times as many.”

The impact was immediate: restrictions loosened, and a rebounding scallop industry turned New Bedford into America’s highest-earning fishing port, a distinction it has held for more than 20 years now.

But government regulators say the cod fishery is different. Russ Brown, a scientist at the National Oceanographic and Atmospheric Administration, said the latest science shows Atlantic cod stocks are still a shadow of their former selves.

“We’re at less than 10 percent of the biomass we were seeing historically,” Brown said.

Adding to the debate surrounding cod are some new, stricter regulations going into effect this fishing season. NOAA now requires full-time surveillance of groundfish boats, either through cameras or in-person monitors. Regulators have said they need to keep a closer watch to make sure fishermen are really catching what they say they are, as there have been infamous cases in the past when fishermen snuck illegal catches past regulators.

The move to full-time surveillance has stirred up resentment in an industry where many fishermen say they’re punished for fluctuations in fish counts while government regulators chronically underestimate the amount of cod in the ocean.

Fishermen tend to view Stokesbury, the scientist who shook up the scallop fishery, as a more accurate voice. They donate boats, captains, food and fuel to help keep costs down on some of his research expeditions. The state of Massachusetts provides additional funding.

But some scientists are more skeptical than Stokesbury about the cod fishery’s potential to recover. One of them has an office down the hall from him.

Professor Steve Cadrin, a fisheries scientist with a key role in an ongoing review of how the government assesses cod stocks, said the cod fishery has opened up prematurely once before.

“We've seen other year classes that have not survived,” Cadrin said.

Some years, Cadrin said NOAA’s projections have been overly optimistic.

“They led to continued overfishing and the stock hasn't rebuilt,” Cadrin said. “It's a lot more than just a heartbreak. There's been a lot of fishery restrictions because of that.”

Codfish are also up against climate change and rising sea temperatures, which affect how fast they grow and how much they spawn. Cadrin said it will take years of additional data collection in waters beyond the Gulf of Maine to determine whether the class of cod Stokesbury is tracking can germinate a broader rebound of the species.

Stokesbury and the fishermen invested in his findings are intent on gathering that data. His team departed from New Bedford Thursday morning for a third year of surveys on a ship called the Justice.

Cadrin’s working group at NOAA will decide later this year whether Stokesbury’s research on cod should go into next year’s stock assessments.

Ben Berke is the South Coast Bureau Reporter for The Public’s Radio. He can be reached at Follow him on Twitter @BenBerke6.