According to the game's art director Lou Catanzaro, Blue Fang Games (who were huge fantasy fans, including The Lord of the Rings) wanted to create an expansion pack for Zoo Tycoon themed around "Fantastic Creatures", as preluded to by the Unicorn and the Yeti being unlockable or downloadable animals. This would ultimately never materialize, as the development team decided it was "risky" and that the more realistic animal packs were more in line with the game's core audience.

According to the game's art director Lou Catanzaro, Zoo Tycoon was originally pitched to Hasbro Interactive before it was pitched to Microsoft. Hasbro Interactive passed on the game, while Microsoft would agree to publish it.

Before creating Zoo Tycoon, the developers at Blue Fang considered creating an airport themed simulation/management game. This idea was quickly rejected by the company's president Hank Howie, who felt that a successful "Tycoon" game would need to center on a fun and engaging place like the theme parks seen in RollerCoaster Tycoon. At the suggestion of employee Brian Shea, they settled on a zoo management game instead.

One of the bonus downloadable animals Blue Fang developed and released for Zoo Tycoon was the mythical Yeti, although there is evidence that it was originally planned to be an unlockable Easter egg animal in the base game, similar to the Unicorn and Triceratops. An unused cheat code exists where the Yeti would have been unlocked by naming an exhibit "Kathmandu", the name of the most populous city in the landlocked South Asian country of Nepal located in the Himalayas, where the Yeti was purported to have inhabited in legend.

During the development of Zoo Tycoon, Microsoft held an online promotional competition called the "Beast in Show", where fans could vote for a real-life zoo animal to be included in the game. Out of the ten nominees, a polar bear named Magnet won the competition and was included as a downloadable animal. Magnet was born in 1988 and lived most of his life at the Maryland Zoo in Baltimore. He received his name based on the way he stuck to his mother's side and became highly popular with guests, often being seen playing with his favorite red ball.

In-game, Magnet essentially functions just like the regular polar bear, with the primary differences being a slightly different model with a cream-colored coat and having an additional distinct animation where he plays with his red ball. Oddly, despite being a real-life animal, Magnet is still treated as a standard, adoptable animal in-game, which means that it is possible to adopt multiple Magnets that can also be female. Magnet would later pass away on April 28, 2015 at age 26, after suffering from complications from kidney and liver disease.

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".

Before the release of the Zoo Tycoon: Dinosaur Digs expansion pack, the Triceratops held the distinction of being the first ever prehistoric creature featured in the Zoo Tycoon series, as a hidden unlockable animal within the first base game: Players could unlock it 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, the Triceratops' sprite is modified to appear smaller and less vibrant; 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.

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 "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.

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.

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 hidden aquatic animal, the mythical Mermaid, that is unlocked through a method unlike any other animal in the game.

Among the new scenery options is a Mermaid statue that can be placed inside marine tanks. When placed, the statue shatters to reveal a living Mermaid that had been sealed within, which then behaves just like any other aquatic animal in the game.

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.