The Zoological Museum grew from the Natural History Cabinet of Kazan Imperial University. However, some its collections are even older that the University itself. In late 18th century Prince Grigory Potemkin-Tavricheski planned to establish a university in Yekaterinoslav (now Dnipropetrovsk, Ukraine) and bought collections of animals, plants, and minerals. By the order of Emperor Pavel I in 1798 the collections were transferred to Kazan Gymnasium, the school that served as the basic institution for the later establishment of Kazan University. The collections then had 133 items.

Professor Karl Fuchs was the first museum administrator. He decided to buy a collection of 578 seashells from Professor Bronner.

Professor Eduard Eversman contributed immensely to the Museum's growth between 1828 and 1860. Under his watch the Museum became a systemized collection of zoological items with 5,735 depository entries in 1844.

Professor Nikolay Wagner, famous zoologist, took charge in 1860. He was also an excellent child story writer, creator of a classic Russian book of short stories “Tales of Purry the Cat”.

Alexander Butlerov, famous chemist, community leader, Rector of Kazan University from 1860 to 1863, was a fan of botany and zoology since youth. His graduation thesis was dedicated to butterflies of the Volga-Urals region. He donated his collection of 1,151 butterflies to the University in 1881. The Museum’s entomological room displays a part of his collection.

Many Mediterranean invertebrates were brought to Kazan by its employees who worked at the Naples Marine Biology Station in mid-19th century. Such are luminous Pelagia, rainbow-colored sea mouse, and extremely dangerous Physalia. Most of these items are made by zoologists Meyer, Ousov, and Livanov.