The Pacific Legal Foundation on Aug. 2 filed notice of its intent to appeal the decision. In its opening brief filed Monday with the U.S. Court of Appeals for the Ninth Circuit, the PLF asks that U.S. District Court Judge John C. Coughenour's June 13 order be overturned and that NOAA be ordered to rewrite the hatchery policy.

The judge's order said the Endangered Species Act was designed to protect "naturally self-sustaining populations in their naturally-occurring habitat."

"Though it scarcely seems open to debate, the Court concludes that in evaluating any policy or listing determination under the ESA, its polestar must be the viability of naturally self-sustaining populations in their naturally-occurring habitat," Coughenour wrote.

"We want it thrown out but for entirely different reasons" than the parties that first challenged the hatchery policy, PLF attorney Sonya Jones this week. The Building Industry Association of Washington, Washington State Farm Bureau, Coalition for Idaho Water and Idaho Water Users Association, which PLF represents, say the policy improperly distinguishes between naturally spawned and hatchery born salmon and steelhead of the same species.

"The ESA does not allow a government agency to artificially exclude species members from a population when those members meet NMFS’s population criteria," according PLF's opening brief. "Under the ESA’s clear terms, NMFS must treat equally, without distinction, all members of a species it includes in a species population.

"Likewise, under the ESA, NMFS may not artificially subdivide a population into two separate populations, as if they were different species, when all the members of the species meet NMFS’s population criteria," according to the Aug. 10 filing.

Trout Unlimited and other fishing and conservation groups challenged the policy and its application to Upper Columbia steelhead, saying the hatchery fish should not be included in stocks being considered for ESA protection. NOAA in 2005 used the newly developed policy in evaluating the status of the Upper Columbia steelhead stock. It determined that the steelhead should be downlisted, from endangered to threatened.

The federal government included hatchery stocks in nearly all of the 25 West Coast salmon and steelhead "evolutionarily significant units" it evaluated following the legal invalidation of its Oregon Coast coho listing, and a 1993 "interim" hatchery policy NOAA used in making that determination.

The re-evaluation of existing West Coast listings, which concluded in 2005 and 2006, included in the listings hatchery stocks that were not more than moderately divergent genetically from naturally produced fish and that were not judged a risk to the wild fish. Hatchery fish, identified by clipped fins, within the ESUs were not afforded the same protections from harvest or "take" as naturally born salmon and steelhead. The determinations focused on the status of wild populations and evaluated how they might be affected, positively or negatively, by their hatchery kin.

"The Final HLP is the product of a thorough deliberative process in which NMFS addressed the difficult question of how to account for the contributions that well-run hatchery programs may have in conserving self-sustaining natural populations, while also recognizing the threats that they may pose," according to a Justice Department brief filed with the district court early this year.

Federal attorneys will again defend the policy and listing determinations. The Justice Department filed on Sept. 7 its notice of intent to appeal Coughenour's order.

The Ninth Circuit had established a briefing schedule to debate the merits of the PLF appeal. The fishing and conservation groups, represented by Earthjustice, are scheduled to reply to the PLF's opening brief by Oct. 11. But the schedule for the three-cornered debate will likely be changed with the federal government now added to the mix, Jones said.

The PLF says hatchery and naturally produced salmon that share the same watersheds and genes should be counted as one when assessing population status.

"In sum, NMFS fails to employ the proper standard for determining whether salmon populations warrant listing as threatened or endangered species under the ESA and, if listed, the appropriate recovery role for hatchery salmon," according to the PLF brief. "The ESA requires that NMFS treat equally all salmon it includes in a salmon population, without regard to where or how individual members spawn or reside."