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Recreational anglers seeking summer flounder in New York waters this year will face the most stringent restrictions yet on their catch and when they can fish.

The new regulations come as the state pursues a lawsuit challenging federal fisheries rules it says unfairly limit New York's share of summer flounder, a mainstay of Long Island's recreational fishing industry.

The 2009 limits announced Wednesday by the state Department of Environmental Conservation will curtail the recreational summer flounder season by about a third. The season will be split into two parts - from May 15 to June 15, and again from July 3 to August 17.

The new daily bag limit restricts anglers to two fish, down from four. Each fish must be at least 21 inches long, a half-inch increase from last year.

"The limits that we have set - with the input of the fishing community - are not ideal but are the best compromise for all of New York's anglers under the severe federal restrictions," DEC Commissioner Pete Grannis said in a statement.

The prospect of a monthlong shutdown at the height of the tourist season did not please Dennis Kanyuk, a Point Lookout captain who is also president of the industry group United Boatmen of New York. "A lot of charters were already booked," he said. "It really screws up three weeks of your calendar."

But Jim Gilmore, DEC's chief of marine resources, said the move was an effort to ensure all the region's charter and party boats could operate during at least a part of their usual season. Boats out of the North Fork catch much of their summer flounder - also known as fluke - in May, while those along the South Shore do bigger business in July and August, according to Gilmore and local captains.

"You're never going to please everybody; there aren't enough fish to go around," said Capt. Joe McBride of the Montauk Boatmen's & Captains Association.

The problem began in the early 1990s, when a federal plan to rebuild declining fluke numbers set quotas for each Atlantic state based on historical catch data.

New York, which gets about 17 percent of the coastwide recreational landings, contends the data are obsolete and favors neighboring states such as New Jersey, which got a larger share. New York anglers have repeatedly exceeded the recreational quotas in recent years, triggering penalties that force even more drastic restrictions on the fluke catch.

"It's causing us as managers to do some things we shouldn't be doing" to comply with federal regulations, Gilmore said. Among them: upping size limits so that more fish are discarded than kept, increasing fish mortality and also targeting the biggest, most fertile females.

"The bottom line is that antiquated and arbitrary federal rules have tied DEC's hands, and it's going to sink Long Island's fishing industry," Sen. Charles Schumer (D-N.Y.) said.