The National Marine Fisheries Service and the U.S. Fish & Wildlife Service have rejected a request to list the Atlantic sturgeon — the largest native fish in the Chesapeake Bay — under the Endangered Species Act.

But the decision will almost certainly trigger a legal challenge from the group that petitioned to have the sturgeon, whose populations have plummeted all along the coast during the past 100 years, listed as a threatened species.

“I’d say there’s a 99 percent chance we’re going to challenge them in federal court,” said Jasper Carlton, director of the Colorado-based Biodiversity Legal Foundation. “It’s critically endangered. To say it is not even biologically threatened is incredulous.”

The Atlantic States Marine Fisheries Commission, which is responsible for managing migratory species along the East Coast, in June closed the Atlantic sturgeon fishery for the next four decades to allow the population to rebound.

Federal officials said that action contributed to their decision.

“There is no doubt that Atlantic sturgeon have been severely overfished,” said Jon Rittgers, acting NMFS Northeast regional administrator. “But the range-wide prohibition on harvest and possession in all the coastal states recently formalized as a long-term moratorium by the Atlantic States Marine Fisheries Commission has removed that threat to the species.”

Ron Lambertson, USF&WS Northeast regional director, said that “with the complete closure of the fishery, we are confident that populations will be increasing. Restoration of this slow-maturing fish will be a lengthy process, and firm commitments to the necessary long-term protections are already in place.”

But Carlton said the ASMFC’s action, by itself, would do little to help the sturgeon because it failed to improve habitat by curbing pollution in spawning areas, or limit the bycatch of sturgeon in fisheries targeting other species.

“If you’re not going to list the Atlantic sturgeon and the Atlantic salmon under the Endangered Species Act, at least as threatened, you might as well not have an Endangered Species Act,” said Carlton, whose organization has also been active in seeking to have the Atlantic salmon listed in New England.

“They’re just not going to list anything that’s water-related because water is the big issue,” he said. “They don’t want to have to address water pollution, habitat destruction and overfishing, and all three of those apply to the Atlantic salmon and the Atlantic sturgeon.”

Sturgeon can grow up to 14 feet long, weigh more than 800 pounds and live up to 60 years. They are an anadromous fish, spawning in freshwater rivers but spending most of their lives swimming along the coast until returning to their native rivers to spawn. They were once one of the most important fisheries in the Bay and along the coast, but sturgeon take so long to reproduce — females don’t mature for more than a decade — that their population was unable to withstand fishing pressure and was nearly wiped out in the early part of this century.

Although sturgeon fishing has essentially been banned in the Bay for years, scientists have observed no evidence of a population rebound. The only river that has shown evidence of occasional spawning is the James.

Nonetheless, a status review team with biologists from USF&WS, NMFS and three state agencies, concluded that the species is neither threatened nor endangered. The team concluded that spawning populations remained in 14 East Coast rivers, and possibly five more. Historically, the fish spawned in 34 rivers. Also, the team said habitat conditions in the rivers were gradually improving.

Carlton expressed doubt about the conclusions. “I’d be amazed if they can back this up,” he said.

He said a river that occasionally has a sturgeon spawning in it — as may be the case in the James — is no indication of a healthy, abundant stock.“I’d be delighted if indeed they can show me they have two or three healthy viable populations.”

Carlton said the failure to list the sturgeon and improve its habitat conditions would lead to more species becoming imperiled. He said his organization may seek to have a dozen East and Gulf coast species listed under the Endangered Species Act in the next two years. “This is going to initiate fish wars on the Atlantic Coast,” he said.