The state has lost an important battle with the federal government over the listing of Atlantic salmon in eight rivers as endangered.

U.S. District Court Judge Gene Carter issued a decision Thursday in favor of the federal government, saying that the scientific and legal arguments for listing the fish as endangered are sound.

The decision could mean an end to nearly a decade of fighting over the salmon’s status and the beginning of a much-needed recovery effort, said Jeff Reardon of Trout Unlimited, one of many conservation groups that have advocated salmon protection under the federal Endangered Species Act.

“It’s sort of a race to see whether the fish are going to exist when this argument is over with,” Reardon said Friday. “We don’t have much time.”

Former Gov. Angus King had vehemently opposed the listing since it first was proposed in the mid-1990s.

Despite state efforts, however, the federal government declared salmon endangered in eight Maine rivers in November 2000. They are the Dennys, East Machias, Machias, Narraguagus and Pleasant rivers in Washington County; Cove Brook, a tributary of the Penobscot River in Penobscot County; the Ducktrap River in Waldo County, and the Sheepscot River in Lincoln County.

The decision declared Atlantic salmon in the eight rivers a “distinct population segment,” a term meaning that Maine’s salmon are valuable because they are genetically distinct from their Canadian relatives.

At King’s direction, the state filed suit against the U.S. Fish and Wildlife Service and the U.S. Marine Fisheries Service in December 2000, arguing that their decision to list salmon was motivated by environmentalists’ threats to sue, not by sound science.

Days later, a coalition representing the state’s business community – the Maine State Chamber of Commerce, Atlantic Salmon of Maine, Stolt Sea Farm Inc., the Maine Aquaculture Association, the Maine Pulp and Paper Association, the Wild Blueberry Commission, Jasper Wyman and Sons, and Cherryfield Foods – joined the lawsuit.

Aquaculture interests fear that the endangered species listing could lead to new restrictions that might drive them out of business. Federal scientists have expressed concern that farmed salmon of European descent could escape and interbreed with native, endangered fish.

As the status of Maine’s salmon has been debated, the state already has lost $15 million in aquaculture investments, Sebastian Belle, executive director of the Maine Aquaculture Association, said Friday.

Blueberry farmers feared having strict restrictions placed on the amount of irrigation water they may withdraw from the protected salmon rivers.

Judge Carter decided that neither fear gave businesses the right to second-guess the federal agencies’ decision, and ruled that the businesses lacked legal standing.

The plaintiffs are disappointed but have not decided whether to appeal, Belle said.

Carter did agree to hear the state’s arguments, but on each point sided with the federal agencies.

The state argued that Maine’s salmon couldn’t be declared endangered because of impure bloodlines. Hundreds of non-native salmon have been stocked in Maine rivers over the past century. Truly wild salmon may not even exist, according to the state.

State lawyers contend that the ESA listing is illegal and unfair because this alternative viewpoint was not considered.

Carter decided federal scientists met their responsibility by providing sufficient data to back up their decision, and he chose not to make his own scientific determination.

“The court is not in a position to make policy judgments based on conflicting or uncertain scientific or technical data,” Carter wrote.

The state may appeal the loss, but as of Friday afternoon, no decision had been made. Attorney General Steven Rowe is expected to make his decision within a few weeks, according to Assistant Attorney General Chris Taub.

Gov. John Baldacci has not followed King’s lead in the salmon crusade. Nor has he spoken in favor of the ESA listing. The governor did not choose to withdraw the state’s lawsuit after taking office in January.

Friday afternoon, Baldacci met with his natural resources commissioners and representatives from the Attorney General’s Office to consider the state’s next move, said spokesman Lee Umphrey.

Baldacci agrees that the endangered species listing is bad for the state, but an administration spokesman said, “It may be time to move on,” according to an Associated Press report Friday.