HARTFORD — Jeff Wilcox is shutting his 135-year-old family marine supply business in Stonington, a casualty in the battle over federal fishing limits.As fishermen are sidelined, taking their boats out of service for lack of work, New England’s marine industry that repairs, stores and cleans boats is next in line to feel the hit. Wilcox, owner of Wilcox Marine Supply, blames the federal government and the fishing limits it’s imposed. In Stonington, he said, the number of draggers — fishermen who drag nets behind their boats —has dropped since the mid-1990s from 50 to two. His business, which employed 13 people in the early 1990s, has dwindled to just himself.“It’s put almost all the fisheries out of business and now it’s trickled down to me,” he said.Many southern New England fishing communities face a similar problem. Richard Fuka, president of the Rhode Island Fishermen’s Alliance, warns that if the fleet continues to be diminished, “Rhode Islanders could see a local heritage industry slip away and become a museum piece.”John Bullard, the Northeast’s top regulator at the National Oceanic and Atmospheric Administration, has said sharp cuts in fishing catches are painful but necessary to help fish stocks rebound.The most significant fishing cut is a 78 percent year-to-year reduction in the catch of Gulf of Maine cod. Fishermen also are forced to take in fewer key flounder and haddock species. Fishery scientists have said some species are recovering far too slowly, requiring cuts in catch to meet mandates to end overfishing and rebuild fish stocks.Fishermen have criticized science they say has underestimated the health of fish stocks. Because of the rules, which are the subject of a lawsuit filed last May by Massachusetts Attorney General Martha Coakley, fishermen say they can’t catch enough fish to stay in business.Michael Fusillo, who teaches economics at Tufts University, said a business downturn at port services would cause ripples through the industry, reducing the supply of fuel, drivers who deliver the fuel and workers who weigh and cut fish.“It’s not just the owners and crews that are losing out here, but the connected industry on the supply side that’s affected as well,” he said.The number of state-licensed commercial vessels in Rhode Island dropped from 1,790 in 2005 to 1,619 in 2012, a 10 percent decline, according to the state Department of Environmental Management. The number of licensed boats edged up slightly from 2011 to 2012.In Massachusetts, the number of permits issued to commercial boats fell by 3 percent from 2009 to 2013, to 5,066, according to the Executive Office of Energy and Environmental Affairs.Viking Gustafson, general manager of Gloucester Marine Railways, a shipyard in Gloucester Harbor that’s been in business since before the Civil War, said the industry has consolidated in response to the catch limits. “Boats have been sold, boats aren’t fishing,” she said.On a recent weekday, the shipyard employed six workers, “which is a few too many because we don’t have demand for services,” Gustafson said. That’s down from 10 several years ago and dropped to three on Thursday.The port service stores boats in dry dock, pressure washes, welds and repairs boat hulls and vessels. While the loss of business is directly due to what Gustafson called a “severe cut in groundfish,” she said it followed years of other regulatory actions that have caused a decline in business.Connecticut waters, which are not subject to federal catch limits because the adjacent Long Island Sound is a Connecticut-New York body of water, imposed its own limits to protect fish stocks, said Mark Alexander, supervising fisheries biologist at the state Department of Energy and Environmental Protection. The state imposed a moratorium on certain fisherman licenses.“If the (fish) population rebounds, we don’t want to see a huge influx of people jeopardizing the recovery,” he said.A decline in commercial fishing vessel permits is due to factors such as older fishermen leaving the business, fewer lobsters, the federal catch limits for offshore boats and permit fee increases, Alexander said.Jeffrey Stieb, executive director of the Port of New Bedford, said the port is doing well as it diversifies to include vessels bringing in scallops and clams in addition to groundfish.Brian J. Rothschild, president of the Center for Sustainable Fisheries, said the number of fishing vessels has declined by as much as 30 percent in the last three or four years, with groundfish catches falling from 140,000 tons to 30,000 tons.He said Coakley’s lawsuit could spur needed improvements in fishery management.“Fish populations have a way of going up and down, and industries have a way of responding to those changes,” he said.Wilcox, who recently turned 65 and has worked since 1972 at the business his great-grandfather founded nearly a century earlier, said he doesn’t know what he’ll do next. “It’s sad. There’s no reason for it except that the government can do it,” he said.