Completing the "Paradise Island" scenario will reward the player with the mythical Unicorn as an adoptable animal. However, it can be unlocked earlier by renaming an exhibit to "Xanadu".

The name "Xanadu" seems to be a reference to at least one of the following:

•The former capital of Shangdu, which featured unicorns on its currency during the Yuan dynasty.
•The 1980 film Xanadu, a musical fantasy.
•The 1988 comic book series also called Xanadu, which featured unicorn characters.

One of the dinosaurs introduced in Zoo Tycoon's first expansion pack, Dinosaur Digs, is the Caudipteryx, a small bird-like dinosaur from Asia. In-game, it is listed as hailing from the Jurassic era, and it's even one of the dinosaurs the player is required to adopt in the "Jurassic Zoo" scenario, which hence its title, requires utilizing all of the game's Jurassic era dinosaurs to win. This is an error on Blue Fang's part, as the Caudipteryx actually hailed from the early Cretaceous period.

The adoption icon and information plaque for the mythological Yeti lists them to be from the Arctic instead of the Himalayas.

Completing Zoo Tycoon: Dinosaur Dig's final scenario, "Breeding the T-rex", will reward the player with the Deinosuchus as an adoptable animal. However, it can be unlocked earlier by naming an exhibit "Super Croc".

Predating Zoo Tycoon: Dinosaur Digs, the Triceratops is notably the first ever prehistoric creature included in the Zoo Tycoon series as a hidden unlockable within the first base game. Players could unlock it as an adoptable animal by completing the "Breeding the Panda" scenario, but it could also be unlocked earlier by renaming an exhibit to "Cretaceous Corral".

Notably, with the installation of the aforementioned Dinosaur Digs expansion pack, the Triceratops' sprite is modified to be much smaller in size and duller in color; it also now functions like the other dinosaurs, such as now requiring to be hatched out of an egg and be taken care of by a scientist (as opposed to a zookeeper), and will break out of all fences from the base Zoo Tycoon game.

One of the "Ice Age" (aka Pleistocene) era prehistoric creatures introduced in Zoo Tycoon: Dinosaur Digs is the "Giant Tortoise". In real life, as mentioned in its in-game description, its name is Meiolania.

Strangely enough, Dinosaur Digs depicts the Giant Tortoise as a tundra-dwelling reptile, perhaps to give it parity with its fellow Pleistocene/"Ice Age" animals such as the Woolly Mammoth, Sabre-Tooth Tiger (aka Smilodon) and Woolly Rhino, that all share the Tundra biome. In real life, the Meiolania actually lived in warmer, sub-tropical habitats such as prehistoric Australia.

If you place a Lion, a Bengal Tiger and a Grizzly Bear into an exhibit, you will get a yellow brick path to use. The item description says "Yellow brick paths indicate to guests where they should walk, especially scarecrows, lions and tinmen"; a reference to The Wizard of Oz.

Zoo Tycoon's second expansion pack, Marine Mania, includes a secret aquatic animal, the mythical mermaid, that is unlocked within a very unique method that no other animal is.

One of the new scenery pieces included in Marina Mania is a mermaid statue. This statue is place-able in marine tanks, and doing so will the cause the statue to break, revealing a living Mermaid that was trapped inside, which will then function as any other aquatic animal.

If a herbivorous animal is placed into an emperor penguin exhibit, the penguins will attack and eat the animal. After this occurs, the penguins will attack and eat any animal that is placed in their enclosure.