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The premise was that the earth was about to be destroyed, and some alien race could only save one species. Much to the chagrin of the humans, they saved the most intelligent species which turned out to be dolphins. It's not The Hitchhiker's Guide to the Galaxy, which is everybody's first suggestion. It's not Rescue Party by Arthur Clarke, either.

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    Welcome to Science Fiction & Fantasy! This might help you to improve your question: How to ask a good story-ID question? – Stormblessed Jan 10 at 23:51
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    Was it a short story? What age was it targeted towards? – Stormblessed Jan 10 at 23:52
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    "So Long and Thanks for All the Fish!" :) – m1gp0z Jan 11 at 15:06
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    It doesn't quite match your suggestion, since the Earth isn't in danger, but also worth checking out is Gordon Dickson's "Dolphin's Way" in which a man theorizes that aliens are waiting until humanity proves itself by communicating with Dolphins (a nonhuman intelligence in their own backyard) and then the aliens will make contact and bring humanity into galactic society. Only when the breakthrough comes, the aliens only make contact with the dolphins and bring them into galactic society, leaving humans alone. – starpilotsix Jan 11 at 22:10
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Could it be one of John Varley's Eight Worlds stories? Aliens almost destroy humanity because they recognize dolphins and whales as intelligent but humans as vermin.

Described at length in The Ophiuchi Hotline, the Invaders are inhabitants of gas-giant planets like Jupiter. They transcend the limits of four-dimensional spacetime and can manipulate time and space at will. They classify living beings in one of three categories: those such as themselves, who arise in gas giant planets everywhere, cetaceans such as dolphins and whales, and vermin, the last category including all sentient beings other than Invaders and cetaceans.

The Invasion of Earth was carried out to protect cetaceans from the effects of human civilization. Although no humans were directly killed, billions died as the Invaders dismantled all the infrastructure needed to support human civilization on Earth. The human population remaining on Earth after the Invasion is about the same as in prehistory, living in tribes without access to technology. This is a scenario that has been played out for millions of years across the galaxy. Inevitably the human species will be forced out of the Solar System altogether, to live between the stars where other displaced intelligences are already in residence.

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