NOAA's National Marine Fisheries Service spent a year reviewing a petition to delist the orcas. The petition was brought by the Sacramento-based Pacific Legal Foundation on behalf of California farmers who faced water restrictions to protect salmon the orcas eat. They argued the Puget Sound orcas were part of a larger north Pacific population and didn't qualify for the 2005 endangered species listing.
But NOAA spokesman Brian Gorman said those arguments were rejected.
"We have decided these killer whales are a distinct population group," Gorman said. "They have their own language, own food source. They don't interbreed with other groups of killer whales. They meet the legal standard for a distinct population group."
He added officials are continuing to work on recovery plan options.
There are now 82 orcas in three pods -- J, K and L -- which also spend much of the year in the Pacific off the West Coast.
They are known as southern resident orcas. Puget Sound also is visited by so-called transient killer whales that hunt harbor seals.
"It's great news that Puget Sound's orcas will continue to be protected," said Miyoko Sakashita, oceans director for the Center for Biological Diversity in San Francisco.
"It was troubling to even think that the killer whales might have their protections stripped," she said in an email.
The Fisheries Service says there's no new information to make it change its opinion.
"Our determination that the southern resident killer whale population constitutes a distinct population segment under the Endangered Species Act and previous conclusion that the DPS is in danger of extinction and should retain endangered status all support our finding that the petitioned action to delist the southern resident killer whale DPS is not warranted," the service said in its finding.
Despite their popularity with whale watchers and symbolic value to the region, the orcas are "not in the best of shape," Gorman said.
Their numbers peaked at close to 100 in the 1990s.
"Water quality in Puget Sound isn't the best. There's lots of boat traffic, especially in the summer," Gorman said. "Their food -- Chinook salmon are limited. And that's just in Puget Sound. We have no idea what goes on in the ocean where they spend most of their time."
A recovery plan issued in 2008 suggests actions to address threats from pollution, vessel traffic and noise and a limited food supply, NOAA said in a news release.
A lawyer for the Pacific Legal Foundation said he'll check with the family-run farms to decide whether the next step will be a lawsuit. The Empress Del Bosque and Coburn Ranch farms in the San Joaquin Valley south of Sacramento might receive no irrigation water next year in order to help protect salmon in the Sacramento River.
"Although we disagree with the service, the finding does tee up various issues that we would like to litigate over," attorney Damien M. Schiff said Friday.
The main one is the lack of a genetic difference between Puget Sound orcas and others that are not endangered.
"Our argument is the service is cherry picking to list a population of species," Schiff said. "You could take any species, and if you focus on a narrow subset of individuals you could decide they are not doing well and need protection."
Only by narrowing its focus to these three pods can the service say it looks like the population is in trouble, he said.
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