massachusetts democrats are close allies of the environmental community, routinely receiving top scores on environmental scorecards and leading the charge on major environmental legislation in Washington.

But don’t tell that to Peter Shelley, senior counsel at the Conservation Law Foundation in Boston, or Tom Lalley, oceans communications director of the Environmental Defense Fund in Washington.

They are fighting hard to maintain strict federal limits governing what Massachusetts fishermen can catch on the grounds that the restrictions are the only way to restore depleted stocks of cod, flounder, and other species. Their sworn enemies in the fight are not just the fishermen of New Bedford and Gloucester, but also US Reps. Barney Frank and John Tierney, Democrats who represent those communities in the House, and Demo­crat John Kerry and Republican Scott Brown, the Bay State’s senators. Gov. Deval Patrick, another political ally of the fishermen, made a personal appeal in January to his friend President Obama to ask him to intervene on behalf of the fishermen.

It’s a situation that leaves Shelley “perplexed and disappointed.” Lalley takes it less personally. “It’s hard to make assumptions about where members of Congress will stand on fishing,” he says. “It tends to be a constituent services issue.”

But the Massachusetts representatives insist that it’s they who are in the right, defending an ancient way of life against rules that they believe will drive small fishermen out of business. The catch limits, they insist, are based on flawed science and should be higher.

“I don’t see an environmental issue here,” says Frank. “We’re not talking about making the ocean dirty. We’re not talking about fouling the air. We’re not talking about anything that degrades the environment. The debate is over how many fish you can catch without depleting the stock.”

The issue has simmered for years but came to a boil over last year’s rules implementing a 2006 law that requires an end to overfishing by 2011. The rules, which are set by a regional fishery council for New England that reports to the Com­merce Department in Washington, set a total allowable yearly catch for each fish species, with quotas established within each species for individual fishermen. It’s called a “catch share,” which fishermen can use, lease, or sell—something like a cap-and-trade system for fishing.

Environmental groups say the catch share system holds the greatest hope of rebuilding depleted stocks after numerous other approaches—time limits forcing fishermen to spend more time at port, temporary closures of prime fishing grounds, and limits on the use of the most efficient fishing gear—have mostly failed.

But Massachusetts’s main fishing ports, New Bedford and Gloucester, are suing the Commerce Department to overturn the rules. They fear that small businesses won’t have enough capital to stick it out when the catch limits are most strict and will be forced to sell their shares to bigger operators, only to see the catch shares rise in value when fish stocks recover.

“For too long, self-interest, environmental ex­tremism, and undue influence from special interests have shaped [the fishery] council decisions,” says New Bedford Mayor Scott Lang, whose city’s fishing catch, principally scallops, is the most valuable in the nation.

Frank and Tierney filed a friend of the court brief supporting Lang’s lawsuit last year. Frank calls the catch shares system a consolidation measure. “I don’t see why environmentalists should be in favor of fewer small independent people,” he says.

The debate has become so heated that last year Frank and Tierney called on the Obama administration’s top fishing regulator, Jane Lubchenco, the head of the Com­merce Department’s National Oceanic and Atmos­pheric Administration, to resign. She is a former board member of the Environmental Defense Fund, one of the environmental groups most enthusiastic about the catch share system.

Frank later backed off, but was front and center last fall when he and Gov. Patrick met in Boston with Lubchenco’s boss, Commerce Secretary Gary Locke, to urge him to raise the limits. Locke, who has since been nominated as US ambassador to China, got an earful from local fishermen as well and pledged to consider carefully whether to raise the catch limits.

The fishermen’s hopes were dashed in January when Locke wrote to Patrick and Frank to say his hands were tied. Frank, not normally someone to call fellow Demo­crats to account, blasted Locke for a lack of  “courage.” He also suggested Locke’s actions may make him less supportive of Obama administration initiatives in Congress.

At the root of the dispute is whether Commerce’s predictions of collapsing fish stocks are, in fact, true. Brian Rothschild, a professor of marine science at the Univer­sity of Massachusetts Dartmouth, says that catch limits are at least 30 percent too low for most species and that Commerce could allow the state’s fishermen to pull an additional 100,000 tons of fish out of the water, valued at about $30 million, without negatively impacting conservation goals.

The law “says you take economics into account as well as the pace at which you replenish” the fish stocks, Frank adds, setting a 10-year deadline for replenishing the stocks. “We’ve said: ‘If it’s going well, and we’re making progress, why not 12 or 13 years?’”

But environmentalists see the problem as far more precarious. And they point to New England’s signature fish as a prime example. A study by professors at the Univer­sity of New Hampshire found that the cod population on Georges Bank, about 60 miles off of Cape Cod, would need to expand by nine times to reach a healthy level.

The overfishing problem began, in environmentalists’ view, a century ago when steam-powered trawlers first took to the seas off New England. In the 1950s, regulations restricted the size of nets the trawlers could use, only to be circumvented by foreign ships that swarmed the waters off New England.

It wasn’t until the early 1970s that international rules took effect. Later that decade, Congress passed the Magnuson-Stevens Act, which declared US control over waters out to 200 miles from shore and set up a system of regional fishery councils to regulate the industry. But the law also provided government tax breaks for US fishermen to upgrade their boats, leading to more overfishing.

Fish stocks continued to drop, a Commerce Depart­ment history of the New England fishing industry contends, “in the wake of ever-advancing harvesting technology, and failure of the management system to take steps necessary to rebuild the populations.”

Environmentalists say rebuilding began in earnest in 2006 when Congress revised the Magnuson-Stevens law, and set a strict deadline to end overfishing by this year. The Obama administration has pushed regional fishery councils to adopt the catch share system, which has seen success in other fisheries.

All this comes at a time when the fishing industry, whatever its struggles, is still big business in the Bay State. According to a federal report issued last year by the Com­merce Department’s National Marine Fisheries Service, Massachusetts fishermen pulled in 326 million pounds of fish, worth $400 million, in 2008. The state’s fish were sold at retail for nearly $4 billion, supporting more than 73,000 fishing industry jobs. By contrast, the state with the largest fishery in the United States, California, saw fishing contribute $4.7 billion to its economy and support 160,000 jobs. Florida was the only other state to see more economic impact from fishing than Massachusetts.

Shelley acknowledges that the catch share system will cause at least some short-term pain for many fishermen, and that it will lead to some consolidation in the industry. But he says that’s nothing new. Previous restrictions limiting the number of days Massachusetts fishermen could be at sea had the effect of cutting the number of active boats in half between 2001 and 2009, from about 1,200 to around 600, he points out.

Advocates of catch shares hope that they will ultimately lead to not only greater efficiency, but a healthier fishery, albeit one that supports fewer fishermen. They figure it may only take a few years before Massachusetts begins to see healthier stocks of key species like cod and flounder.

And environmentalists aren’t without allies in the  fish­ing community. In fact, it was the 2,500-member Cape Cod Commercial Hook Fishermen’s Association that first lobbied the regional fishery council to adopt an experimental catch share system in 2004. The association says it sees benefits in a system that allows fishermen to fish when they want, eliminating the rush to sea that occurred when old rules set specific fishing seasons. And they hope that will also reduce temporary price fluctuations that accompanied seasonal oversupply.

Environmentalists worry, though, that the system could fail if there isn’t enough enforcement of the quotas. Only 30 percent of Massachusetts boats are staffed with observers, leading to ample opportunity to cheat.

Heightened enforcement is not in the offing, given the pressure Bay State lawmakers are bringing on the Com­merce Depar­tment to ease off. And not without cause, environmentalists admit, given last year’s report by the department’s inspector general, an independent watchdog at the agency, which found that Commerce had been particularly tough on Massachusetts fishermen who’d violated fishing limits. The report prompted the agency to reassign its top enforcement officer in the state.

Bay State lawmakers led by Tierney, Frank, and Kerry pushed Commerce in January to allow fishermen who’d missed a deadline another chance to appeal their cases. Locke initially turned down the request, enraging the law­­makers and Patrick. “It’s a bad decision. He does have discretion and it’s unfortunate he’s chosen not to use it,” Tierney said at the time.

Patrick wrote directly to the president later that month, asking him to overrule Locke. “The fishing families of Massa­chusetts deserve better,” he wrote.

In March, Locke and Lubchenco eased the appeal pro­cess after a meeting with Kerry. The arrival of new White House chief of staff William Daley has also given the lawmakers some renewed hope. Daley, as commerce secretary in the 1990s under President Clinton, worked with them on easing restrictions on harvesting scallops. Frank says he expects he’ll prove receptive again. “We are talking about working people feeling some pain,” says Frank.