His knowledge, reputation, and international contacts allowed him to set up a very extensive plant collection.
The collecting of tropical (from the Indies) and sub-tropical (from the Cape Colony) plants was continued under Clusius' successors.
During that period he collected many dried and living plants from all over Japan (as well as animals, ethnographical objects, maps, etc.
From its original plan the Hortus was expanded in 1736 by Adriaan van Royen and Carl Linnaeus, and in 1817 by Theodor Friedrich Ludwig Nees von Esenbeck and Sebald Justinus Brugmans.
A reconstruction of Clusius' original garden, based on a plant list dating from the end of the 16th century, was opened in 2009.