The University of Leiden featured one of the first botanical gardens north of the Alps, which was fully equipped in 1594. The first three persons responsible for the garden—Carolus Clusius, Dirk Outgaertsz. Cluyt and Pieter Pauw—had to distribute the plants and herbs into the different garden beds. The logic behind the spatial order they chose gives insight into various approaches on plant classification in the early modern period. It is possible to reconstruct and analyze the order of plants using catalogues from different years. These catalogues show the changes in the distribution of plants under the prefecture of several natural historians. The catalogues themselves are an interesting historical source, showing a way to transfer a garden and its plants into a printed counterpart. In the early modern period, the classification of plants was not yet strictly defined. Also, in the botanical garden of the University of Leiden, we do not find a single, stern systematic approach to ordering the plants, but rather a number of different ones. Plants were classified according to their virtues and to empirically comprehensible criteria, but also according to their beauty or even to the chapters of an herbal. The reconstruction of the distribution of the plants shows those different approaches to ordering the flora and casts light on the development of botany.