The Department of Invertebrate Zoology houses some of the most extensive and historically important metazoan and protozoan collections available to researchers today. The Department also contains the arachnid collection, but excludes mollusks, insects, and most of the fossil invertebrates. And in July 2016, the deuterostomes and the "lophophorates" formerly within the MCZ’s Department of Marine Invertebrates were added to the Department. The holdings today represent well over one million specimens within approximately 350,000 lots, nearly 8,000 primary types, plus several thousand secondary types. The Araneae collection is currently one of the largest in the world, with all major families represented. The crustacean collection is among the most important in the world. Other strengths are the Acari (including fossil material in Baltic amber), Myriapoda, Cnidaria and hexactinellid sponge collections. The echinoderm collection is type-rich, and is also one of the largest in the world.
The collections contain terrestrial and aquatic specimens from diverse geographical regions of the world. Many specimens were collected during the 19th and early 20th century expeditions, most significantly the “Thayer” to Brazil, the “Hassler” around the coast of South America, the “Blake” and “Atlantis” both to the Atlantic and Caribbean, the “Challenger” and “Albatross” to many Pacific regions, and the U.S. Geological Surveys of the Territories.
More recent marine acquisitions include North Atlantic specimens from various National Marine Fisheries Service cruises, the reference collection for the Massachusetts Water Resource Association Boston Harbor clean-up and the Howard Sanders deep-sea collections from the Woods Hole Oceanographic Institution.