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The Department of Invertebrates (excluding insects, myriapods and arachnids) has focused its research primarily on the study of marine invertebrates. (This is mainly due to the history of the Danish Kingdom, its navy, its overseas trading activity and its past interest in colonies.) The most important parts of the collections are the type collections, and its cataloguing is still going on. The collection holds many types from the late 18th century and early 19th century as follows:

-the Protozoa section is a rather complete collection of Xenophyophora and other types such as the Foraminifer collection.
-the Porifera collection centers on the North Atlantic, deep-sea worldwide, and Antarctica.
-the Cnidaria section includes the Hydromedusae collection whose coverage is worldwide. The Hydropolyp collection is very representative for the North Atlantic, and this is the case also for both main groups of Anthozoa.
-the Platyhelminthes, Aschelminthes, and Proarthropods section is reflective of the Zoological Museum long history in the study of "Lower Worms" (Platyhelminthes, Nemertina and Aschelminthes) and the so-called Proarthropods (Tardigrada, Onychophora and Pentastomida).
- the "Vermes" (phyla consisting primarily of macrofauna) section houses the collections of five phyla: Annelida (including Pogonophora and thus also Vestimentifera), Echiura, Sipuncula, Priapula, and Chaetognatha. Among them, emphasis in collection and research has historically been placed on the polychaetous annelids.
-the Collection of Mollusks is one of the more important of the large, old collections in Europe, going back to King Frederik III's "Kunstkammer" from the 1650's.
-the Crustacea Collection holds one of the largest and historically most important collections of Crustacea held anywhere in the world. The collection dates back to the immediate post Linnaean period.
-the Entoprocta section contains material from Scandinavia and Florida (USA), including a number of types of the family Loxosomatidae.
-the Ectoprocta = Bryozoa Collection contains large material from all over the world; about two thirds are in alcohol, the rest is dry.
- the rather small collections from Phoronida, Pterobranchia, Enteropneusta, Larvacea sections.
-the Urochordata section containing a large collection with material from many expeditions, including many types.
-the Thaliacea and Ascidiacea sections containing large collections from a number of expeditions.
-the large Echinoderm Collection is one of the three largest collections in the world. It contains some 3731 identified species of the known recent ca. 6300 species in the world, including 613 holotypes and a large number of paratypes. The collection consists of dry and wet specimens, a large number of slides (holothurian ossicles, echinoid and asteroid pedicellariae, larvae and histological sections of a number of echinoderms). The Echinoderm Collection is one of the most valuable documentary collections in the world.
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The collection of Freshwater Invertebrates (insects, crustacea, snails, worms) holds in excess of 1.5 million specimens including over 1000 primary and secondary types. It comprises ethanol preserved specimens in small glass-vials, stored in more than 4500 sealed glass jars; pinned specimens of selected adult insects in unit trays stored in 160 drawers; microscope slide mounted specimens and a photographic record of selected specimens and sites sampled. The collection provides historical records of species with some material dating back to the 1930's. Information on more than 120 000 accessions is recorded in hand written catalogues and on a computer database for ease of access. Several card index systems allow access to publications and specimens, and rapid identification of species from diagnostic drawings.
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The Invertebrate Collections date from the middle of the 19th century to the present. The are some 200 corrals over 100 years old. In addition, check out their Malacology, Entomology, and Herpetology sections.

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The Invertebrates Department's collection is concentrated on localities in the Eastern and Gulf Coasts of the United States. The collection contains dry and alcohol-preserved specimens representing 14 phyla which includes Protozoa, Porifera, Cnidaria,Platyhelminthes, Gastrotricha, Rotifera, Nemata, Nematomorpha, Annelida, Arthropoda, Bryozoa, Brachiopoda, and Echinodermata.

The systematically arranged collection contains 18,000 lots, about evenly divided between dry, alcohol-preserved, and prepared slides of specimens. The collection is strong in the arthropod class Crustacea, particularly the Decapoda, and in the phylum Annelida, particularly the classes Polychaeta and Hirudinoidea. Important taxonomically restricted collections within the overall collections are:

• Edward Potts Collection: Porifera (Spongillidae)
• L. M. Dorcy Collection and Rotifera J. Percy Moore Collection: Annelida (Polycheata, Hirudinoidae)
• Joseph Leidy Collection: Parasitic Organisms (Nemata, Nematomorpha), and
• Felix-Edouard Guerin-Meneville Collection: Crustacea
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