References and Further Information: 1  Morrissey, J.F. and J.L. Sumich. 2012. Introduction to the Biology of Marine Life (10th Edition). 2  University of California Museum of Paleontology. Bilateral (left/right) Symmetry.
A lot of things. For one, Whale sharks are fish and use gills to breathe. Blue whales are mammals. The blue whale is also bigger than the whale shark. The tail structure is also different if you watch the whale shark swim, it uses its tail in a side to side motion while the blue whale uses a up and down movement.
In fact if you exclude the cetacean species (whale, dolphins and porpoises) the whale shark is the largest living animal in existence, in regards to length. The average male whale shark grows to just over 30 ft in length although there are reports of whale sharks growing well over 40 ft.