Even before checking his lobster traps, Anthony Coviello knew they wouldn't be brimming with the snapping, squirming crustaceans that would greet him on a typical autumn fishing day. Of that he was sure. The lobsterman was out on the water mostly to satisfy himself that Long Island Sound still hadn't unleashed its elusive harvest--the fall lobster run that fishermen awaited this year in vain.

So when one lone lobster, shiny black and red, wriggled forlornly from the boxy trap Coviello had hauled onto the boat, there was a "whaddyaknow" shrug from the four lobstermen aboard.

"She's slow," Coviello said, noting the lobster's lethargic demeanor. "Usually this trap would have 30 lobsters, with five to six keepers," he added while heaving aboard the next empty cage, its rotten bait a testimony to the lobster paucity.

"We're going out, hoping there will be something. But in reality, deep down inside, we know we're finished." As Coviello spoke, a dozen languid seagulls skimmed the otherwise empty waters off Greenwich, Conn., where lobster boats typically dot the Sound on this late November day.

As far east as Branford, Conn., and across to the shores of Long Island, N.Y., the lobsters have all but disappeared from Long Island Sound, the 120-mile-long estuary wedged between Long Island and the mainland coast of Connecticut and New York. Beginning at summer's end, a strange phenomenon struck, more widespread and deadly than a lesser trend last fall, when dead and sick lobsters turned up in traps by the thousands. In November and early December, when the busy "fall run" should have been in full swing, there was for the most part nothing. A little one here and there, a droopy one in a trap, but basically the lobsters were gone. Even worse, fishermen said, the lack of juveniles boded ill for future years, when they would anticipate catching them at legal, full-grown size.

"This is the worst anybody's ever seen," said Nick Crismale, head of the Connecticut Lobstermen's Association and a 27-year fisherman. He said his business is off 60 percent. Despite other bad years from time to time, "this is the first time I'm not able to pay my bills," said lobsterman Frank Fernandes of Long Island. He stopped fishing in September when his traps reaped a 50 percent mortality rate and eventually took a job driving for UPS.

"We don't even bother to send the truck to the dock anymore," said Richard Pomasan, a New Jersey-based distributor who typically purchases 9,000 pounds a day from Sound fishermen hauling as much as 500 pounds each. With his business off 80 percent, Pomasan is fishing for crabs to make ends meet.

What is killing the Sound's $43 million-a-year lobster catch, the nation's third-largest? New York and Connecticut officials, the National Marine Fisheries Service and biologists hired by the lobstermen are compiling microscopic clues. But scientists say it could take years to determine the true culprit, which may be some combination of environmental stresses, such as gradually warming water and pollutants.

So far, University of Connecticut scientists have implicated a single-celled parasite called a paramoeba, which also has afflicted blue crabs. Veterinary pathologist Richard French said the parasite inflamed the nervous systems of the lobsters he examined, but it does not sicken humans.

Separately, biologist Michael Loughlin of the Maine Lobster Institute detected a type of bacteria in the sick lobsters called "gram negative rod" bacteria, similar to a type that previously afflicted Maine and Canadian lobsters. Conversely, however, blood studies at the National Marine Fisheries service lab in Milford, Conn., showed no bacteria, officials said. Nor did a University of Arizona lab find any evidence of viruses.

Even if further tests finger the paramoeba, "there's nothing that says necessarily that this is the only thing," said Gordon Colvin, director of marine resources for the New York Department of Environmental Conservation. "Nor does it necessarily explain the questions of why here, now. We have a lot more work to do to get at those more complicated underlying questions."

For example, what conditions have made the lobsters susceptible to the fatal agent that also is targeting sea urchins and crabs? Pollutants are obvious suspects. Environmentalists contend that pollution from sewage discharges has severely undermined the Sound's marine health, particularly in the western end.

Longtime fishermen such as Carlo Dimeglio say that two decades ago even the East River bordering Manhattan yielded lobsters, and waters off the Bronx were bountiful. "That's been dead for six or seven years," Dimeglio said.

State officials have linked a harmful summer depletion of dissolved oxygen in the Sound to man-made and natural conditions. But the trend doesn't resolve the lobster mystery, because this summer's incidence was no more severe than in other years, said Eric Smith, assistant director of fisheries for Connecticut's Department of Environmental Protection. Nor did recent testing unearth more toxins than usual in the Sound. Further, a sophisticated photographic device found nothing amiss in bottom sediment, and scientists have ruled out a bacterial infection called gaffkemia, which hit the lobsters in the early 1990s.

Roger Tollefsen, president of the New York Seafood Council, said lobsters that his seafood outlet purchased from fishermen last spring were "voraciously" hungry, leading him to suspect a problem in their feeding cycle.

Some even suspect the die-off may be linked to the lobster proliferation that has given fishermen boom harvests in recent years. "One of the many hypotheses you need to consider is whether a dense lobster population is contributing to its own demise," by accommodating the rapid spread of disease, said Colvin.

There's little effect on restaurants, distributors say, because Canada and Maine are still the big suppliers. Maine and Massachusetts together harvested 60 million pounds of lobster in 1998, compared with Long Island Sound's 11 million pounds. But the fishing industry and the Sound are the focus of concern.

"The handwriting is on the wall," said David Leff, Connecticut's deputy commissioner of environmental protection. "We can see our fishermen are in distress. The lobster fishery has pretty much collapsed."

The Commerce Department is weighing requests from Connecticut and New York for disaster assistance to help the fishermen and to conduct research into the cause of the die-off. Congress would have to approve the allocations. "I think of them as farmers who are impacted and need help to get through a bad period," said Rep. Christopher Shays (R-Conn.), who promised to push the fishermen's cause.

Any help won't come too soon for the lobstermen, who are still smarting from last year's slowdown.

"We're not just a bunch of fishermen crying about a bad year. We're fishermen who have been at this a lifetime and suddenly the rug has been pulled out from under us," said Robert Vissa, joining Coviello on the glassy waters out of Greenwich's Cos Cob harbor. "Five years ago, I would have said we've got a paradise here. It was really a great place to fish."