The narrative below surveys some of the major holdings, but is not intended to be a comprehensive description. Various specimens of fish, amphibians, reptiles and mammals that are on display in the MCZ's public exhibition areas are available for research access by pre-arrangement.
The collection represents a spectrum from the earliest known vertebrates to late Tertiary teleosts. The collection was established by Louis Agassiz who brought with him considerable European material initially obtained for the Natural History Collections of Harvard College. In the 1860's, Agassiz purchased a large number of British Paleozoic sharks and rhipidistians from the famous collection of the Earl of Enniskillen. The Marder collection, also British Paleozoic sharks, was obtained at about the same time, as was the C. F. Hartt collection of Cretaceous teleosts from Ceará, Brazil. Alexander Agassiz acquired a number of important additional collections in the 1880's. Among these are the Haeberlein collection of exquisitely preserved fish and other vertebrates from the lithographic limestone at Solenhofen; the Terrell collection from the Cleveland Shale, including the giant arthrodire Dinichthys; the Stock collection of fish from the Scottish Coal Measures; and Sternberg's collection of predaceous teleosts, some very large, from the Cretaceous Niobrara chalk. Sizable acquisitions of Eocene teleosts from Wyoming and Monte Bolca, Italy, were also the gift of Alexander Agassiz. A large quantity of Devonian fish from Iowa, and Silurian and Devonian ostracoderms from Scotland and Scandinavia, represent major holdings of early material. Additionally, there are smaller collections of jawless fishes, including the Patten collection, from a number of other localities in North America and Europe. Palaeoniscoids are represented by an extensive series of forms from the Devonian of Scotland, Lower Carboniferous of North America and England, Upper Carboniferous of North America, Permian of England and Germany, and Upper Triassic of North America. During the 1890's and early 1900's, C. R. Eastman added a quantity of important North American Paleozoic fishes.
Devonian dipnoans, arthrodires and osteolepids from Scotland, Devonian arthrodires and rhipidistians from Quebec, a Carboniferous fish fauna from Cape Breton, and dipnoans, rhipidistians, sharks and other fish from the Permian of the American southwest were added by A. S. Romer in the mid-20th century.
Other smaller collections have been added from time to time, including specimens of exhibition quality from North America, Europe and Australia, crossopterygians from the Carboniferous at Linton, Ohio, and a collection of Triassic fish in nodules from Madagascar.
Early acquisitions include stegocephalians from the lower Permian of Lebach, Germany, (originally part of the Bronn collection) and from the Linton Coal Measures of Ohio; anurans from the Miocene of Germany; and finally, well preserved material of Eryops, Buettneria, and Diplocaulus.
The Sternberg collection from the Permian of Texas, obtained in 1882, contains important specimens of Seymouria, Captorhinus and Diadectes. Additionally, the MCZ acquired classic specimens of Jurassic crocodilians and Triassic ichthyosaurs from England and Germany, Triassic phytosaurs from the American west and southwest, and giant plesiosaurs from Australia.
Of principal importance is a diverse faunal collection from the Triassic of Brazil and Argentina, including cynodonts, dicynodonts, rhynchosaurs, archosaurs as well as various amphibians. Additionally, the MCZ holds a representative sample of the Rhaeto-Liassic fissure fill fauna from Bridgend in England, as well as a select representation of various groups, including mosasaurs, dinosaurs and pterodactyls. Elements of the early Cretaceous fauna of the Cloverly Formation of Montana include a number of dinosaur specimens, several of them nearly complete, as well as lizards, amphibians and dwarf crocodiles. The early Jurassic fauna of the Kayenta Formation of northeastern Arizona is represented by archosaurs (dinosaurs, pterosaurs), tritylodontids, turtles, sphenodontids, frogs and caecilians.
The MCZ's collection of fossil birds, previously held in the Ornithology Department, have been transferred to Vertebrate Paleontology. A few specimens are European in provenance, but most are North American, and include material from: the Cretaceous Niobrara Chalk; the Eocene Green River Formation; the Oligocene of Goshen Hole, Wyoming; the Lower Miocene, Agate Springs, Nebraska; and mid-Pliocene deposits of Florida.
A modest assortment of mammalian fossils was deposited by Louis Agassiz. Alexander Agassiz subsequently made major acquisitions through the purchase of Garman and Clifford's collections from the White River Oligocene and the Pleistocene of Nebraska, Sternberg's collection of Pliocene rhinoceroses from Kansas, and Schlaikjer's diverse Oligocene and Miocene materials from Wyoming, South Dakota and Nebraska. Major faunal collections are those from the Miocene at Thomas Farm, Florida, from the Paleocene at Shotgun Butte, Wyoming, and from the Cretaceous at Bug Creek, Montana.
Less extensive faunal collections are from the early Eocene Willwood Formation of Wyoming, the late Eocene Uinta Formation of Utah, and the Oligocene Jebel el Qatrani Formation (Fayum, Egypt). Other holdings from North America include the Earl Douglass collection of cetaceans from the Tertiary of South Carolina, the Moreno collection of ground sloths, and Cuban Pleistocene material, chiefly rodent, obtained by Barbour, Brooks and Warner.
The Rossignol collection of Eocene mammals represents one of the unique holdings of fossil mammals in the MCZ, for the quarries from which these well preserved specimens were obtained have since been destroyed. The collections of Duval, Bronn and Eser also represent the European Tertiary with both types and other specimens. In addition, the collection has modest assemblages of fossil mammals from the Tertiary of South America, including several complete specimens, and a small collection of Australian marsupials.
Mesozoic mammals are represented by a collection of cranial and postcranial elements of Morganucodon obtained through exchange with the University Museum of Zoology (Cambridge, England), Dinnetherium nezorum from the early Jurassic Kayenta Formation of northeastern Arizona, and Gobiconodon ostromi and triconodontids from the early Cretaceous Cloverly Formation of Montana.