There's a fish in the Columbia River Basin in Montana and Idaho called the cedar sculpin, or Cottus schitsuumsh. It lives in waters that are well known and fished, but it's newly discovered.
It's a rare event, but it does happen.
Back in 2000, a new species of bass, Micropterus cataractae, was even
described from well-known and commonly fished rivers of the southeastern United
States. Fishermen had known of the
“shoal bass” for at least fifty years, but no scientific examination had been
made to see if this fish differed from other bass. A large shoal bass can be two feet long and
weigh over eight pounds.
That was the case for a long time with the sculpin, too. The new find was a "cryptic species" - an animal that looks so much like related species that it needs expert examination to distinguish it. The cedar sculpin, it turned out, had a single tiny visual difference from the shorthead sculpin, Cottus confuses. DNA is increasingly the tool of choice for distinguishing species, but it's not a perfect science yet. What degree of difference splits a species off from the others? While this is still being worked out, this article describes an effort to determine the true diversity of fish and amphibians in the rivers of the Rocky Mountains. What's known so far is that we've considerably underestimated it.