When the museum opened in 1904 its collections were primarily based on natural history specimens. These included many zoological specimens from the Cleveland Lit & Phil Naturalist's Field Club, the hunting collections of A.E. Pease and a collection of birds purchased by H.W.F. Bolckow in 1874. In 1918 the T.H. Nelson collection of birds and eggs were bequeathed and put on permanent display. During the late 1960s to early 1970s when the museum was part of Teesside Museums Service a large number of zoological specimens were transferred to the newly established School's Museum Service. It was during this time that the main galleries were redisplayed changing the emphasis from natural history to local history although the Nelson Bird Room was kept. Due to the fragility of the materials most of the extant zoological collections are now held in store and only displayed for short periods in special exhibitions. A few large mounts can be seen in the shop area, including the museum's adopted emblem - the A.E. Pease lion.
The museum’s zoological collections still represent the major part of its holdings, numbering in excess of 150,000 specimens. The bulk of the collections are made up of invertebrates, especially molluscs and insects.