“The islands don’t have as diverse marine life as, say, Indonesia, because they’re so far north,” extending up to the latitude of New Orleans, said Russell Brainard, NOAA’s chief coral reef scientist in Hawaii. “But in terms of their size and the low level of interference from man, they’re already unique.”

With the exception of highly militarized Midway and Tern Island during World War II, the 10 islands or island groups have been nature reserves of one sort or another since President Theodore Roosevelt established the Hawaiian Islands Reservation in 1909. Today, under the tutelage of Fish and Wildlife Service biologists, the islands are slowly recovering from the depredations of humans and the plants and creatures they introduced, including rabbits, rats and ironwood.

What some jokingly call the second Battle of Midway began innocuously enough early in the second Clinton administration, when Interior Secretary Bruce Babbitt hired William Y. Brown, a former chairman of the Ocean Conservancy, and asked him to look into expanding the department’s role in protecting the oceans.

Image The atoll is home to many marine species, including spinner dolphins. Credit... Linny Morris for The New York Times

“It became clear that the most important coral reef complex in American waters that needed protection was the Northwest Hawaiian Islands,” Mr. Babbitt said in an interview.

The Interior Department includes the Fish and Wildlife Service, which had already banned fishing in the archipelago’s near reefs to a depth of 60 feet. Beyond that, the first three miles of water belonged to the State of Hawaii, which opposed an end to fishing, according to the Democratic governor at the time, Benjamin J. Cayetano. The waters extending from there to 200 miles were managed by NOAA, which is part of the Commerce Department.

Dr. Brown recalled that the islands were being intensively fished for lobster, and that Fish and Wildlife Service officials in Honolulu were saying there was nothing they could do about it since the fishing was in waters deeper than 60 feet. A second, smaller fishery of bottom fish like pink snapper and Hawaiian grouper was also being depleted, he said.