The Natural History Museum of Crete is organized in 7 Divisions:
- Botany
- Geodiversity
- Paleontology
- Vertebrates
- Invertebrates (except Arthropods)
- Arthropods
- Genomics and Genetic Resources
it has two Laboratory Units:
- Education
- Ecology – Environmental Management
and maintains a permanent exhibition – educational space on Sofoklis Venizelou Avenue (Dermata Bay) on the beach front of the city of Heraklion.