Well, the coelocanth, an ancient fish said to be extinct for over 100 million years, was discovered in the 20th century. Recently, a small school of about 500 Coelocanth were found off the coast of Africa. Because they are so scarce, and hold historic significance because of their lizard-like fins, they are deemed a "legendary" fish.
Same with the Pokemon. In the games, they're unique, but in the anime, they are extremely scarce, and have cultural, Religious, and/or historic meaning. Ever notice how all of the legends, even in the older seasons, were based around Legendary Pokemon?
It's for these reasons that both Pokemon, and animals, are deemed legendary, even if they aren't unique.