Anglers took home just 15,000 winter flounder from the local bays during the 2007 fishing season, an extraordinary drop from the nearly 5 million caught in 1987, Mr. McAllister reports in "Baywatch," the baykeeper's most recent assessment of the bays' health.
"Until stocks rebound, stop fishing" said Mr. McAllister, who attributes much of the decline to subpopulations of winter flounder living off-shore in the deeper, colder waters of the Great South, Moriches and Shinnecock bays, where they are vulnerable to draggers.
"Once the Peconic subpopulation is lost, it won't be replaced by Shinnecock Bay's," he added.
The state Department of Environmental Conservation limits anglers to 10 winter flounder a day with a minimum length of 10 inches. A department spokeswoman would not address whether the DEC would consider a fishing freeze on winter flounder.
The DEC "remains very concerned about population numbers and trends," the spokeswoman, Maureen Wren, said. "We will continue to closely monitor the situation."
Regulations, though, will not reverse the drop in winter flounder numbers, said Charles Witek, chairman of the Coastal Conservation Association.
"Regulations didn't stop the bleeding. Regulations don't stop overfishing," said Mr. Witek, who earlier this year released a winter flounder population study to the DEC. Mr. McAllister based some of his assessment on Mr. Witek's study.
"Adult fish from various subpopulations mix in deeper, cooler waters during the summer, where they are subject to harvest by commercial trawlers," Mr. Witek wrote. "Most of New York's waters have already lost nearly all of their adult flounder populations."
Local fishermen were split on the idea of a winter flounder fishing ban.
Regulations already have burdened the industry, said Charlie Manwaring, a fisherman who owns Southold Fish Market in Southold.
"Regulations have hurt us all," said Mr. Manwaring, who doubts a complete shutdown will ever occur. "It's stupid to throw dead fish [that are too small] back into the water.
Mr. Manwaring said the low numbers of winter flounder have more to do with spawning and habitat, not overfishing.
"Winter flounder don't come into Peconic Bay anymore," he said. "If you weren't born in the bay, you're not going to come back."
Doug Rogers, who has been fishing out of Orient Harbor since 1973, said he hasn't targeted winter flounder for the past few years. He believes a fishing freeze could help.
He said his bread-and-butter fish these days are bluefish, porgies and fluke -- and that he's never seen so many fluke in his life.
"You can't have an abundance of all species of fish all the time," he said.
Southold Trustee and career lobsterman Jimmy King said he's noticed that the resources for winter flounder are "historically low."
"Sometimes a moratorium is necessary," he said. "They did it with Atlantic sturgeon."
But Mr. King's brother, Mark, who has been fishing out of Mattituck Inlet for 40 years, cautioned against a ban.
"One thing leads to another," he said, referring to continued commercial regulations on striped bass and other species that have replenished in recent years.
Mr. Witek said he doesn't understand why the winter flounder population has not been monitored until now.
"The failure to properly manage winter flounder is the great mystery of fishing in the Northeast," he said. "People see bluefin tuna collapsing, and the environmentalists are up in arms. Winter flounder is disappearing, and people yawn."