Estonia was occupied and annexed by the Soviet Union in 1940, delaying the planned development of the zoo.

The zoo has two tropic houses which include crocodiles and other reptiles, as well as fishes, exotic birds, marmosets, chimpanzees, and mongooses.

It houses snakes, African elephants, two black rhinos, pygmy hippos, armadillos, and rodents.

The Middle-Asia Complex was built in 2002, and includes animals such as Przewalski's horses, Bactrian camels, bison, yak, and hyaenas.

Tallinn Zoo is working on a European mink mission to release these endangered animals to wild.

In late 2007, a polar bear escaped from its cage due to human negligence, and died after being tranquilized.