The Zoological Research Garden started out as the Biological-Pedagogical Institute, established in 1931 in Yehuda HaLevi Street in Tel Aviv, by the naturalist and educator Yehoshua Margolin. The goal of the Institute was to train nature teachers to educate Israeli children. At the heart of the Institute lay the belied that knowing and understanding the natural world is the best way to connect people to their land.
Yehoshua Margolin was the director of the Institute until his death in 1947. His successor was Prof. Heinrich Mendelssohn, who had immigrated to Israel in 1933 and received his PhD thesis from the Hebrew University. Mendelssohn contacted Margolin, started to work with him, and after Margolin's death became the new director of the Biological-Pedagogical Institute.
After the 1948 War of Independence, Tel Aviv's city council proposed that Prof. Mendelssohn choose a larger place to host the Institute. After examining several options the Institute moved to Abu-Kabir, to a building originally meant to serve as a hospital.
In 1953, the Academic Institute for Natural Sciences was established, headed by Prof. Mendelssohn. In 1956 the Institute was joined to the Institute for Humanities and became a University – Tel Aviv University. The Zoological Garden became a part of the Zoology Department in the new university, and continued to expand and grow as the research and teaching infrastructure for nature research at Tel Aviv University.
In 1981 the Zoological Garden moved to its present location on the university campus in Ramat Aviv.