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HALF MOON BAY, Calif. — Stevie Fitz, a commercial fisherman, was pulling up his catch in one of his favorite spots off of Point Reyes in June when he saw something terrifying — in his nets were nearly 300 bocaccio, a dwindling species of rockfish protected by the government.

There are such strict limits on catching the overfished bocaccio that netting a large load, even by accident, can sideline and even ruin an independent fisherman.

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Still, Mr. Fitz did not try to hide his mistake by slipping it back into the deep. Instead, he reported himself. With a few swipes on his iPad, he posted the exact time and location of the catch to a computerized mapping system shared by a fleet of 13 commercial boats, helping others to avoid his mistake.

“It was a slap in the face,” he said, “but we are trying to build an information base that will help everyone out.” He was later able to sell the bocaccio, although the catch still counted against his quota for the year.

A lifelong fisherman, Mr. Fitz is part of a very unusual business arrangement with the Nature Conservancy, an environmental group that is trying to transform commercial fishing in the region by offering a model of how to keep the industry vital without damaging fish stocks or sensitive areas of the ocean floor.

Five years ago, the conservancy bought out area fishing boats and licenses in a fairly extreme deal — forged with the local fishing industry — to protect millions of acres of fish habitat. The unusual collaboration was enjoined to meet stricter federal regulations and the results of a successful legal challenge. But once the conservancy had access to what was essentially its own private commercial fishing fleet, the group decided to put the boats back to work and set up a collaborative model for sustainable fishing.

Bringing information technology and better data collection to such an old-world industry is part of the plan. So is working with the fishermen it licenses to control overfishing by expanding closed areas and converting trawlers — boats that drag weighted nets across the ocean floor — to engage in more gentle and less ecologically damaging techniques like using traps, hooks and line, and seine netting.

The conservancy’s model is designed to take advantage of radical new changes in government regulation that allow fishermen in the region both more control and more responsibility for their operating choices. The new rules have led to better conservation practices across all fleets, government monitors say.

“It is blowing me away what is happening out there,” said William Stelle, the administrator for Pacific Northwest region of the National Oceanic and Atmospheric Administration’s marine fisheries service. But, he added, the conservancy “may be the most sophisticated example of the successful marriage of interests between the environmental community and the fishing industry in marine conservation.” Similar programs are beginning to appear in other places.

American fish stocks have been troubled since the early 1990s and remain so because of overfishing, pollution, and warming seas. The government says that today 23 percent of fish stocks are not at self-sustaining levels at current fishing pressure.

Congress passed a law in 1996 demanding that local fishery councils protect “essential fish habitat.” In 2006, it also imposed tight catch limits for overfished species. As a result, if a fishery exceeds its limit on just one of these species, under federal law, the entire area could be closed to commercial boats for a season.

Local councils have struggled to balance the inherent tensions of adhering to these limits without ruining the fishermen’s ability to make a living. To do this, they have imposed regulations like prohibiting fishing in some areas, dictating the catch season and limiting what techniques and gear are used.

But last year, the Pacific Fisheries Management Council replaced some of those restrictions with strict quotas on six imperiled species and parceled them out among all 138 commercial vessels along the coast. Government observers are now put on every boat to make sure there is no cheating.

The downside is that if one boat lands too much of a sensitive species, known as bycatch, it must be docked until it can buy another boat’s unused quota — and there is not always a market to balance the catch. The quota system also provides incentive for each fisherman in the risk pool to help prevent others from using up their quota. And the early results for fish stocks are promising. Bycatch has dropped from 15 percent to 20 percent of the total haul to less than 1 percent.

The Nature Conservancy first got involved in central California in 2004 when it was looking to invest in marine conservation zones. The group realized that it needed better information to preserve the most critical areas.

“What the fishermen had was a deep local knowledge of the habitats of certain species,” said Michael Bell, senior project director with the conservancy. “There wasn’t scientific information at that level that could match the fisherman knowledge.”

But getting information from fishermen was difficult because they suspected that the conservancy was just looking to close off more prime fishing territory. So to get cooperation, as well as to reduce trawling along as much of the central coast as possible, the conservancy agreed to reduce the potential financial hardship to fishermen by buying the boats or the fishing permits of anyone who wanted out of the business. Thirteen volunteered to sell their permits, and six of the lot also sold their boats for a cost of about $7 million.

The fishermen soon divulged which nurseries and rock formations needed to be protected and which areas where mature fish congregated should be left open. What resulted was a proposal that included large areas of closings — nearly 4 million acres — that most fishermen thought was fair. It was adopted easily by the fishery council in 2006.

It has not been unheard of for environmental groups to buy boats and licenses and then to retire that part of the quota to take pressure off of an area fishery. But it was not an outcome that the fishermen or their coastal towns — Monterey, Half Moon Bay and Fort Bragg — wanted in this case. Rick Algert, the former harbor director for Morro Bay, near Monterey, explained that fishermen were critical to supporting local infrastructure like fuel piers. And besides, he said, “tourists still like to see boats in a working harbor.”

So the conservancy agreed to lease back some permits and boats, but only if their sustainable conditions were met.

Perhaps the hardest one for the fishermen to accept was the automated posting system known as eCatch. But fishermen have come to believe that the data will show patterns — for example, high catch rates of certain species after full moons along the edge of the shallow water shelf in July — that will help them all predict the danger zones. Independent fisherman have joined the risk pool and eCatch system because they see benefits. By handing out free iPads, the conservancy made the posting of real-time results almost effortless.

Their well-financed effort is among the most technologically advanced and coordinated in the country, but others are catching on. In Massachusetts, scallop fishermen, with the help of the University of Massachusetts, have developed a similar reporting program to avoid pulling in endangered yellowtail flounder.

Many of the fishermen have become fans of a system that yields profits and hardly any bycatch. Steve Fitz, Stevie’s uncle, sold their fishing permit to the conservancy and now leases it back. The lease is fair-market value as long as Mr. Fitz continues to use Scottish seining, which is far gentler to the ocean bottom than trawling is.

“The Nature Conservancy had identified that the small family boats were sustainable, and they wanted to help,” Mr. Fitz said. “We recognized that we needed help negotiating this increasingly confusing path into the future.”By LESLIE KAUFMAN, The New York Times