The collections of Cephalonia Botanica were created after numerous botanical expeditions to the Ionian Islands, as well as from the native flora of the Garden itself. In specific sections of the Garden, such as the Urban Garden, foreign Mediterranean species were selected for their resilience to the dry and hot summers of the island. Today, the flora of the Garden includes 350 species, with tree and shrub plants forming a permanent part of the collection, while herbaceous annual or perennial species are chosen depending on what we wish to highlight at any given time.

At the same time, a survey of the native flora of the Garden was carried out, identifying and classifying 200 plant species. The living collection of the Garden now presents over 350 species in the following sections:

1. Shrubs
2. Endemic and Rare Species
3. Bulbs
4. Meadow / Wildflowers
5. Medicinal Garden
6. Urban Garden
7. Lake / Aquatic Species
8. Maquis Vegetation