The Native Great Lakes Fish That Never Came Back

The Great Lakes permanently lost more native fish than most people realize. At least three species are gone outright, two others hang on in only one of the five lakes, and one that spent nearly forty years on the extinct list has just turned up alive. That record sits awkwardly beside the region's better-known comeback story. Lake Erie's recovery is genuine. The algae blooms that made national news in the 1960s and 70s eased, phosphorus loading dropped, and the lake now supports one of the most productive walleye fisheries in the world. But cleaning up a lake does not restore a fish that is already gone, and several of Erie's own natives never returned.

The Blue Pike Collapse Was Almost Unbelievably Fast

The blue pike was Lake Erie's fish. It was not a pike at all but a walleye relative, steel grey-blue and topping out around three pounds. Its eyes were noticeably larger than a yellow walleye's and set higher on the head. Blue pike dinners were as ordinary in Ohio taverns as perch is now.

The commercial numbers show what happened. Nets took more than 3.1 million pounds in 1885. Between 1950 and 1957 the annual catch ran as high as 26 million pounds. By 1959 it was 89,000 pounds. By 1964, dealers moved 200 pounds. That is a collapse from tens of millions to a few hundred pounds inside a decade.

The U.S. Fish and Wildlife Service declared the blue pike extinct in 1983, in the same Federal Register action that delisted the longjaw cisco. Overfishing did most of the damage, compounded by habitat destruction, oxygen depletion in Erie's central basin, and the arrival of rainbow smelt, which likely ate blue pike larvae.

Whether The Blue Pike Was Ever A Separate Fish Is Still Disputed

This is where the story gets genuinely unsettled, and it is worth stating carefully rather than picking a winner.

Carl Hubbs described the blue pike as a distinct species in 1926, then it was demoted to a subspecies of walleye because the two forms intergraded, including in color. Two genetic studies using historic material have since reached opposite conclusions.

A 2014 study in BMC Evolutionary Biology by Haponski and Stepien analyzed mitochondrial DNA and nine nuclear microsatellite loci and found the historic blue pike genetically indistinguishable from walleye, with no unique variation. Their conclusion was that the subspecies designation was not warranted. A separate analysis using nine microsatellite loci on DNA recovered from dried scales collected during mid-century monitoring reported the opposite: assignment tests placed 93.2 percent of blue pike and 100 percent of walleye into their expected groups, which the authors read as genetic separation.

So the honest position is that the blue pike may have been a distinct lineage, or a color morph of a walleye population adapted to deeper, cooler eastern Erie water. Either way something specific was lost, because whatever the taxonomists decide, no fish matching that description has been caught in Lake Erie in sixty years.

The Deepwater Ciscoes Were Hit Hardest

The real losses were less famous. Before the twentieth century the Great Lakes held an endemic complex of ciscoes, small silvery whitefish relatives sold commercially as chubs, that dominated the deep-water prey fish community. Lakes Huron and Michigan were the only lakes that held all six deepwater species plus the shallower cisco.

The deepwater cisco, Coregonus johannae, was among the largest at roughly twelve inches, living between about 165 and 490 feet down in Huron and Michigan and nowhere else. Its size made it valuable once commercial fishing reached it in the 1930s. The last specimens came out of Lake Michigan in 1951 and Lake Huron in 1952. It was the first endemic Great Lakes fish to go extinct.

The longjaw cisco, Coregonus alpenae, took its name from Alpena, Michigan. It was usually netted at 330 feet or deeper in Huron, Michigan, and Erie. The blackfin cisco, Coregonus nigripinnis, is likewise considered lost from the lakes. The kiyi vanished from Lake Huron by 1985 and now persists only in Lake Superior. The shortjaw cisco has been pushed out of every Great Lake except Superior.

One detail explains why this history is so tangled. By 1960 biologists were pulling up specimens that almost defied placement in any species, and started calling them hybrid chubs. As populations crashed, the surviving fish interbred, which blurred the very characters used to tell them apart.

What Actually Killed Them

No single cause accounts for it. Commercial fishing came first and hit hardest, and it worked through the cisco complex by size, taking the biggest species first and moving down as each one thinned out.

Then came the sea lamprey, which reached the upper lakes through shipping canals and fed parasitically on large fish. Rainbow smelt and alewife followed, competing with native fish and eating their larvae. Habitat damage did the rest: dredging, wetland drainage, shoreline armoring, and heavy phosphorus loading through the middle of the century. Hybridization then finished the job on the ciscoes by erasing the distinctions between the remnants.

Lake Ontario's Atlantic Salmon Are The Cleanest Example

Atlantic salmon reached Lake Ontario roughly 12,000 years ago as the ice sheets withdrew, and by the 1700s they were abundant enough to be a staple food and to have towns named after them.

Upper Canada introduced a salmon preservation bill in 1798 and passed it in 1807. Samuel Wilmot built the first government-sponsored fish hatchery in North America at Newcastle, Ontario in 1866. Neither worked. The species was declared extirpated from the lake in 1896, and the last credible record is a seven-pound fish netted near Scarborough Beach in April 1898. Researchers have noted that the salmon went from legal protection to gone in something like fifteen to twenty generations.

Here is why this belongs in an article about fish that never came back. Anglers catch Atlantic salmon in Lake Ontario today. Those fish come from stocking programs drawing on LaHave River, Lac Saint-Jean, and Sebago Lake strains. Canada's own status assessment is blunt about it: the original strain is no longer available, and the native Lake Ontario population, with a history of thousands of years behind it, is extinct. The species is present. The lineage is not.

One Of Them May Have Come Back After All

The shortnose cisco, Coregonus reighardi, lived in Lakes Huron, Michigan, and Ontario. The last one was reported from Lake Huron in 1985, and Canadian assessors concluded that recovery was not feasible because nothing had been seen for over 25 years.

Then, during a Lake Superior survey in 2022, U.S. Geological Survey researchers found three of them. When William Koelz catalogued Lake Superior ciscoes in the 1920s he had listed shortnose cisco among them, and because later scientists never confirmed it, the assumption was that Koelz had made a mistake and the Lake Superior fish were really shortjaw cisco.

USGS presented the finding to the Lake Superior Technical Committee and posted a preprint in April 2025 combining morphological and genetic evidence for the species' presence. Two cautions belong here. That preprint had not completed peer review when it was posted, and USGS declined press interviews pending publication. The same analysis could not resolve the status of shortjaw or blackfin cisco, so those remain open questions. Lead author Owen Gorman put it as a rediscovery in a sense, and noted that nobody expected to find it.

Why It Matters Which Ones Are Gone

The pattern across all of these losses is that the deep, cold, specialized fish went first, and the generalists stayed. Lake Superior kept the most because it was fished later, warmed less, and never took the nutrient load the lower lakes absorbed.

That is not only a historical footnote. Agencies in the United States and Canada are now working to restore ciscoes and bloater to Lake Ontario and the St. Lawrence, and to rebuild deepwater prey fish in Huron and Erie, and Superior is the source population for that work. Which is to say the survivors in one lake are the only remaining material for repairing the others.

The blue pike is not coming back, whatever it was. Neither is the deepwater cisco, and neither is the salmon lineage that arrived in Lake Ontario when the glaciers left. The shortnose cisco appears to be the exception, and it survived not because anyone protected it but because a century-old fish list was right and everyone stopped checking.