In September, Whole Foods launched a color-coded grading system to help customers know whether seafood purchased at the chain’s supermarkets come from sustainable fisheries. Under the grading system, fish species sold at the store with a green rating are considered sustainably caught. A yellow-grade means there are some concerns about the viability of the stock. Red-graded seafood, also labeled as “avoid” species, are overfished and may be caught in environmentally harmful ways.

Along with announcing the new color-coding system, Whole Foods pledges to phase out some red-graded species by Earth Day 2011 and all red-graded species by Earth Day 2013.

But some local fishery experts wonder if the new color-rating scheme will help or hurt consumer confidence in Maine fisheries.

To create the grading system of wild-caught fish, Whole Foods partnered with The Monterey Bay Aquarium and the Blue Ocean Institute. In a press release, Whole Foods officials said they believe the grading system will help consumers make good choices in their seafood purchases. A Whole Foods spokeswoman declined to make store officials available for comment for this story.

While Whole Foods often is seen as influential as Wal-Mart in natural food circles, it still controls a very limited market share in the seafood industry. Patrice McCarron of the Maine Lobstermen’s Association is unconcerned about working lobster into the new color-scheme.

“We have limited resources and we have to be selective about where we focus our attention,” said McCarron.

Whole Foods largely has been an outsider in Maine’s lobster industry ever since 2006, when it first elected to stop selling live lobster out of ethical concerns. The retail chain reversed itself in 2007 and allowed live lobsters in its Portland store. The food chain still sells processed lobster meat at its stores.

The Blue Ocean Institute has been independently analyzing the sustainability of fishery stocks for years, said Dr. Alan Duckworth, a research scientist with the institute. Eighteen months ago, the institute began collaborating with Whole Foods to create a grading system based on those reports. The natural food retailer also paid to have assessments done of species the institute hadn’t yet analyzed.

The institute answers some 60 questions about a species to determine its sustainability, including questions of biology, habitat quality, management practice and potential for bycatch. The peer-reviewed process, which requires synthesizing government reports and academic papers, tends to take about four months.

“It’s a lengthy process, but it’s certainly worthwhile,” said Duckworth.

Duckworth emphasized that the institute operates independent of Whole Foods. He also drew a distinction between the work of third-party certifiers and the work of the institute, saying that his organization compiles reports, but does not offer a seal of approval.

“We’re not a certifying organization,” Duckworth said. “We just simply provide the information.”

But Port Clyde Fresh Catch co-founder Glen Libby worries that such a grading system might unintentionally hurt Maine’s emerging locally-caught seafood movement because it has the potential to lump Maine’s stable fisheries in with less-sustainable fisheries.

“A lot of times, these things tend to paint everybody with a broad brush,” Libby said.

Libby also believes that any sustainability grading system should include how far the seafood travels from the nets to the dinner plate. A grading system that doesn’t calculate food miles discounts the value of local food movements, he said.

But calculating food miles would require tracking individual vendors and require a much greater effort.

“It’s fairly difficult to work that out,” Duckworth said.

The Whole Foods color-coding has won over some previously-skeptical environmental organizations. In the late 80s, Whole Foods and the Earth Island Institute had a war of words over the institute’s attempts to market its turtle-friendly labeling to Whole Foods. But in a recent blog post, the institute’s managing editor, Amy Westervelt, urged readers to cut the retail chain some slack, saying an imperfect grading system is better than no grading system.

“Baby steps, people, baby steps,” Westervelt advised readers.

But some others in the environmental movement are less impressed. Over 2000 people have signed a boycott of Whole Foods for its seafood standards since the new system was announced. Sarah DiGregorio, a blogger for the Village Voice newspaper, recently took Whole Foods to task for continuing to sell unsustainable fish species.

“Displaying the Seafood Watch labels while still selling the species designated ‘avoid’ is having your fish and eating it, too,” DiGregorio wrote.

Many food analysts believe such grading and labeling systems are the trend in food retail, as consumers become more interested in knowing the stories behind the food they eat. A few months before Whole Foods launched its color-coded system, Hannaford Brothers announced it would review its seafood supply chain with the Gulf of Maine Research Institute to ensure the sustainability of seafood sold at Hannaford stores.

Such moves by retail chains is more than altruism, said Duckworth. When it comes to seafood, the chains want to ensure they have seafood to offer customers in the future.

“Supermarkets are for the long haul,” Duckworth said.