The Research Library's holdings include some 20,000 titles in 56,000 volumes, and it currently receives some 700 serial titles from subscriptions and exchanges. Several significant complete or very long runs of both standard and obscure journals are present, on natural history subjects. There is also a collection of 5000 maps, both modern and historic.

Special Collections kept in the Research Library include:

Also housed in the library are 1,094 watercolors of southern California wildflowers by Albert Valentien and 66 watercolors of birds by Allan Brooks and George Sutton. These paintings were commissioned by Ellen Browning Scripps at the beginning of the 20th Century.