The majority of the vertebrate collection is made up of bird specimens, including eggs and nests.
- Birds: About 1,000 specimens mostly mounted or de-mounted, few study skins. Principal collection is that of Thomas Hudson Nelson, author of the Birds of Yorkshire donated in 1918 and mostly on display in a dedicated gallery (see the Nelson Room under the Galleries pages for more information).
- Bird Nests: about 150 specimens including an unusual early 20th century wooden boxed collection with whole clutches transferred from Darlington Museum, collector unknown (to be researched), otherwise mostly single 20th. century acquisitions.
- Bird Eggs: about 3,500 specimens. Principal collection is T.H. Nelson, other smaller cabinet collections. Notable collection of guillemot eggs showing immense colour, markings and shape variations. About 2,500 specimens 19th to 20th century. Many on display in the Nelson Room gallery.
- Mammals: a mixed collection mostly A.E. Pease 19th century material from NE and S Africa comprising skulls, large mounts and trophy heads. Some Australian marsupials acquired for display in the Capt. Cook Birthplace Museum. A few small cased mammals illustrating British wildlife.
- Fish: a small number of fish cast mounts now in poor condition.
- Amphibians: a small number of cased examples mostly British
- Reptiles: a few full mounts including crocodiles, alligator, tortoise etc. Some skins, skulls and turtle carapaces.