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The animal kingdom is divided into two groups based on whether or not a species has a spine: invertebrates do not have a spine and vertebrates do. Invertebrates (Invertebrata) make up about 95 percent of all species discovered until now. The Invertebrates exhibition, on permanent display in the Natural Sciences Pavilion, reflects the size and variety of the world of invertebrates. 

Especially prominent, on account of its historical and scientific value as well as the sheer number of specimens, is the entomological exhibit. The 16,000 insects on display make up only a part of the full scientific collection, which is one of the largest of its kind in the Balkans. The insect exhibit comprises two parts: Insects of the Balkan Peninsula and Exotic Insects.

The exhibit Molluscs of the Balkan Peninsula features 80 representatives of terrestrial and freshwater molluscs of the Balkans, while the exhibit Molluscs of the World features approximately 50 species from the rest of the world. 

Snails and shells of the Mediterranean, 182 species of them, are displayed in two showcases which make up the eponymous exhibit. The exhibit Aquatic, Terrestrial, and Parasitic Invertebrates features 55 species, while the exhibit Arthropods (Arthropoda) features 37 species of scorpions, crabs, and spiders.