The mammal collection in the Yale Peabody Museums’s Division of Vertebrate Zoology, although small, is worldwide in coverage, and is used principally for teaching. The 5,086 mammal skins (over 720 species) date from the 19th century, and includes several rare and endangered species: the African elephant, black rhinoceros, orangutan, mountain gorilla, red wolf, black-footed ferret and snow leopard. The skeleton collection is likewise small (4,776 specimens representing over 770 species), but historically important, and contains a disproportionate number of large animals, among them one of only 7 complete skeletons of the now extinct quagga, and a large series of buffalo skulls from the 1870s.

The fishes collection in the Yale Peabody Museum’s Division of Vertebrate Zoology is worldwide in scope, with an emphasis on marine species. Strengths include: deep sea fishes from the Atlantic and Pacific; Western Atlantic nearshore fishes from the United States, Bermuda, Bahamas, Gulf of Mexico and Caribbean Sea; East Pacific fishes from Mexico, Panama and Peru; Indian Ocean nearshore fishes from Kenya, Sri Lanka, Maldives, Seychelles and Chagos Archipelago; and freshwater fishes from Connecticut, Guyana and the African Great Lakes. Holdings represent over 24,000 specimen lots made up of more than 144,000 individual specimens. Included in this are type specimens for 193 nominal species. The collection includes histology slides and a complete coelacanth specimen.

The Division of Vertebrate Paleontology houses one of the most important vertebrate fossil collections in North America, totaling over 70,000 cataloged specimens. Staff and students of the Division undertake research in vertebrate systematics, evolution, and paleobiology. The Division supports field collecting programs in the Triassic of Arizona and Utah and across the K/T boundary in Montana and North Dakota.

The herpetology collection in the Peabody’s Division of Vertebrate Zoology is worldwide in scope, with over 23,000 specimens and specimen lots (including larvae) of amphibians (over 300 taxa) and reptiles (more than 1,300 taxa). Holdings include 95 type specimens of 8 taxa in both wet and osteological collections.

The Yale Peabody Museum’s paleobotany collection numbers over 150,000 specimens, with 4,200 of these type and illustrated specimens. The collection is worldwide in scope, with approximately 75% of the collection from North America and the other 25% from the Arctic, Australia, Central American, Europe, Israel, Pakistan, Lebanon, South America and the West Indies. Tracing its roots back to the early 19th century, this collection is one of the most historically significant in the United States. Included among its riches are plant fossils from the opening of the American West, from the Wilkes Expedition of 1838–1842 described by James Dwight Dana, Triassic and late Cretaceous floras from New York, New Jersey and southern New England; and the world’s largest assemblage of cycadeoids.

Founded in 1864 by Daniel Cady Eaton from his personal library and plant collection, the Yale Herbarium is an internationally recognized repository with holdings of approximately 350,000 specimens from throughout the world. There are an estimated 3,000 type specimens. The collection is particularly rich in ferns, bryophytes and grasses, as well as in historically important materials from early botanical collectors. In addition, it was the herbarium of record for the flora of southern New England from 1864 until 1955, when that function passed to the University of Connecticut at Storrs.

Primary strengths of the Division of Invertebrate Zoology include large holdings of Western Atlantic invertebrates represented not only by recently acquired specimens, but also by a strong historical component dating to the late 1800s, totaling approximately 3 million individuals, thousands of which are the type specimens of species new to science.

The bird collection in the Yale Peabody Museum's Division of Vertebrate Zoology is among the most comprehensive in North America, with international and historic significance in several areas. The Division's affiliated William Robertson Coe Ornithology Library has an extensive nonlending research and teaching collection of books and journals.

The systematic collections of the Yale Peabody Museum’s Division of Entomology comprise over 1,000,000 curated specimens. Division holdings include important collections of Lepidoptera, arachnids, Orthoptera, Coleoptera, water beetles and midges, and specialty collections on evolutionary themes. Recent acquisitions also include historically important collections from other institutions. The Division also maintains a general entomological library of periodicals, books and reprints that includes coverage of arachnology donated from the Alexander Petrunkevitch Library.

The Yale Peabody Museum's collection of invertebrate fossils is one of largest in the United States, in volume and in geographic, stratigraphic and taxonomic representation. The holdings of the Division of Invertebrate Paleontology represent more than 350,000 specimen lots, approximately 4 million individuals. A total of 35,000 are type specimens; about 4,500 are the basis of new species descriptions. Over 300,000 specimen lots are available in the online specimen index; all known type specimens are included.