The 100m race was set up for Discovery Channel's 29th edition of Shark Week - an annual programming block featuring shark-based shows.
A program schedule released by the channel claimed "the world's most decorated athlete" would take on "one of the fastest and most efficient predators on the planet".
The title for the show 'Phelps vs Shark: Great Gold vs Great White' left many eager to watch the race.
However, instead of racing against a real shark like many anticipated, Phelps was matched against a computer-generated shark with a simulated speed.
Phelps and the shark also swam at separate times - with Discovery researchers first recording the time of the shark before letting Phelps swim by himself in the waters off the coast of South Africa.
Sharks are able to reach around 40km/h with ease, while humans typically reach a top speed of 8km/h in the water.
Phelps was given a wet suit to maximise his speed, however the shark still won by two seconds.
He hinted at a rematch, but many took to social media to voice their anger.
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