For 139 years, the F.J. King haunted Lake Michigan as a rumor.

Fishers said their nets snagged on its bones. A lighthouse keeper swore he saw its masts breach the lake’s surface. Divers searched, and searched again, but always came back from the deep shaking their heads.

The F.J. King became a Midwestern ghost ship: unseen, elusive, taunting.

The mystery grew so big that Neptune’s Dive Club in Green Bay, Wis., offered a $1,000 reward decades ago for its discovery.

And then, on a warm June morning this year, it revealed itself.

On June 28, two hours into a search off Baileys Harbor, Wis., a small fishing town on the Door Peninsula that overlooks Lake Michigan, a sonar screen pulsed with the picture of a schooner.

“We were in disbelief,” Brendon Baillod, the maritime historian who led the search, said in an interview. “We were looking at a perfectly intact schooner lying on the bottom.”

The crew had not set out to find it that afternoon as they went aboard the Shoreline, a tour boat that carries sightseers along the peninsula. The plan was to test a new side-scan sonar with greater capability than the previous one the crew had been using.

The sonar, which was being dragged about 200 feet behind the ship and 75 feet below the surface, emitted waves to map out the dark floor of Lake Michigan. The image it stitched together revealed the unmistakable shape of a 140-foot schooner.

“It was a very dramatic moment,” Mr. Baillod said.

Mr. Baillod said that a key clue leading up to the discovery of the shipwreck was from a newspaper article from 1886, in which the lighthouse keeper provided a more specific detail about where he had last seen the masts of the ship.

Mr. Baillod drew a two-mile-by-two-mile search box around the indicated point, he said, which guided the team’s successful search and eventual discovery.

A small robotic vehicle was remotely piloted into the cold depths to where the wreck appeared to be. The scientists onboard the ship became the first humans to see the F.J. King since it slipped beneath the waves at 2 a.m. on Sept. 15, 1886, as its crew rowed away in the darkness.

The ship had made a hard impact with the bottom of the lake, Mr. Baillod said. The front-right side was crushed, but large wooden anchors remained hanging over the side. Wire rigging trailed down the hull. At the stern, the deckhouse had broken away.

Inside the hull, he said, were the remainders of the crew’s belongings as well as kitchenware scattered across the bottom. The ship’s wheel lay with its handles still intact.

The F.J. King had been a workhorse. Built in 1867 in Toledo, Ohio, for the grain and ore trades, it sailed at a time when highway and rail networks were not yet in place.

The Great Lakes may seem an obstruction “you have to drive around” these days, but at the time “these were our highways,” said Tamara Thomsen, a maritime archaeologist for the State of Wisconsin.

A three-masted schooner, the F.J. King was carrying iron ore from Escanaba, Mich., to Chicago during its final voyage.

But a southeast gale slammed its hull with waves that rose eight to 10 feet, according to the Wisconsin Underwater Archeology Association.

The men pumped furiously until exhaustion set in, but the swells were splitting its seams.

Capt. William Griffin gave the order: Abandon ship.

As the boat pulled away, the crew members watched the rear deckhouse blow off, papers spiraling skyward. Hours later, another schooner rescued them and carried them to Baileys Harbor.

Captain Griffin, certain of his position at the time of the event, later told officials that the F.J. King had gone down five miles offshore, according to the archaeology association. Days later, the lighthouse keeper at Cana Island claimed that he saw its masts nearer to land. Searchers debated for decades which man had been right.

Mr. Baillod bet on the lighthouse keeper. He studied documents, mapped his grid and set his team loose with the sonar. The wreck lay less than half a mile from where the keeper said he had seen the masts.

“It really was a hard ship to find,” he said. “It was not where the captain said it was; it wasn’t where the newspapers said it was. The lighthouse keeper was the only one with an accurate report.”

Remarkably, it rests in one piece, despite its heavy cargo, Mr. Baillod said.

More shipwrecks are being found today than at any time in history. Factors like advances in technology have made it less expensive and more accessible to scan the ocean floor, broadening the search to both amateurs and professionals, archaeology experts say. Shipwreck hunters are more often looking for wrecks for their historical value than plundering their treasure.

Climate change has also played a role, according to experts. The intensified storms and erosion have also helped uncover vessels in shallower waters.

The discovery of the F.J. King is more than a triumph of persistence. It is also an act of stewardship, said Kevin Cullen, executive director of the Wisconsin Maritime Museum in Manitowoc, Wis.

“It’s kind of surreal and humbling to be part of bringing this submerged history to the light of day,” Mr. Cullen said.

The Wisconsin Historical Society has already documented the site with 3-D imaging and plans to nominate it for both the State Register and the National Register of Historic Places. The exact location will remain a secret until then.