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The battle between the fishing industry and conservationists over the depletion of marine life is nothing new, but historian H. Bruce Franklin says things are different this time.

Mr. Franklin says the overfishing of menhaden by industrial and commercial fishermen along U.S. coasts is depleting the species, having devastating effects on coastal ecosystems, especially Chesapeake Bay.

Some researchers deny that the species is headed toward extinction and say the controversy is resulting in major changes in the way fisheries are studied.

Menhaden, a small, silver fish also known as a "pogy," provided $62.5 million in profits to U.S. fishermen in 2005, according to the National Marine Fisheries Service.

Because of their high oil content, they often are reduced in factories to fish oil, fish meal and bait. Products of the reductions also include livestock and pet food, water-resistant paint and cosmetics.

Besides reeling in high profits, menhaden are vital to keeping many ecosystems healthy and clean by eating toxic algae and providing an important food source for bigger fish.

The depletion of once-healthy ecosystems and the loss of menhaden can be attributed to one company, Omega Protein, said Mr. Franklin, author of a book about menhaden, "The Most Important Fish in the Sea."

"The Omega Protein company has a total monopoly on the reduction fishery in the Atlantic. In the Gulf there's one competitor, but the majority of the industry is by Omega," Mr. Franklin said.

Omega Protein, based in Houston, reduces menhaden into animal feed, fertilizer and oil, and is "used in everything from linoleum to health-food supplements," he said.

At one time, Mr. Franklin said, 100 companies were engaged in the reduction industry but most have "fished themselves into extinction."

Ben Landry, deputy director of governmental affairs for Omega Protein, said the company is not overfishing and is committed to maintaining a stable menhaden population.

"Omega Protein is very committed to maintaining a stable menhaden population. That's where our product comes from, and we follow the best available government regulations," Mr. Landry said. "The key contention of the book is that menhaden is being overfished, but all government scientists will repeatedly contend that menhaden are not overfished."

Joseph Smith, a biologist with the National Marine Fisheries Service, said, "Based on the most recent coastal stock assessment that was done on Atlantic menhaden in 2006 with data through 2005, the bottom line is menhaden are not overfished."

Mr. Smith works in a North Carolina lab that studies menhaden along the coast. The lab provides data for and writes the stock assessment reports produced by the Atlantic States Marine Fisheries Commission, the official body appointed by Congress in the 1940s to study and protect menhaden and 21 other species of Atlantic fish.

Bill Goldsborough, director of the fisheries program at the Chesapeake Bay Foundation, said a lot of the menhaden caught by fishermen come from the Bay, making it a good place to study the species.

"I think there is little debate over the fact that menhaden are critical to the ecology of Chesapeake Bay, both in their filter feeding and therefore nitrogen removal and ... in terms of their role as predatory fish," Mr. Goldsborough said.

Mr. Smith said it's hard to determine the menhaden population in the Bay.

"If Chesapeake Bay were a farm pond we might be able to answer some of the questions [Mr. Franklin] and others pose, but Chesapeake Bay is open to the ocean and the menhaden come and go in and out of the Bay," Mr. Smith said.

One of the easiest ways to study menhaden is to study other fish in the Bay that prey on menhaden, Mr. Goldsborough said.

"Striped bass depends heavily on menhaden, with as much as 80 to 90 percent of their diet," he said. "The percentage of menhaden in their diet has gone down tremendously, with lowest estimates at 20 percent."

"We have all these pieces of information that are showing red flags but none of them specifically show cause and effect," Mr. Goldsborough said.

The question of just how many menhaden are in the Bay is a $64,000 question, Mr. Smith said. "There are some research studies going on now that are trying to get at those answers," he said.

Mr. Smith said one study uses airplanes that send low-intensity laser beams into the water to estimate the number of schools. He said this method has proved effective only in clear water and the Bay is far from clear.

"We need to manage fisheries not on a single species, but in a single ecosystem approach," Mr. Goldsborough said.

He said the Bay's main focus is to improve research to ensure accurate data and tools to produce clear results.

"That's what we hope: The research will give them the tools they need to switch to these kinds of studies."

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