The paleontological collections are housed in the Department of Geological Sciences in Physical Sciences South. The collections are divided into two portions - a teaching collection used for instruction introductory and advanced courses, and a research collection, housed separately. The latter collection is further subdivided into a systematic invertebrate collection, a stratigraphic invertebrate collection, a reference collection for the Tertiary invertebrates of the Channel Islands, and a plant collection. In addition, smaller collections reflect the research interests of faculty and graduate students, the largest of these being a collection of Tertiary plant fossils from the northern Sierra. In general, the collection is dominated by marine invertebrates and secondarily by plant material. The limited amount of vertebrate material is largely associated with the teaching collection. Published specimens are generally placed in the University of California Museum of Paleontology at Berkeley; the UCSB collection is largely for reference and educational purposes.

The collection has its roots in the private collection of Alonzo Yates, a recognized amateur invertebrate paleontologist who lived in Santa Barbara a century ago. Yates collected and traded material, assembling a fine small collection of invertebrates, especially Mollusca. He published several new species, and the type and illustrated materials for these descriptions are deposited with the Santa Barbara Museum of Natural History for safekeeping. Other early collections were made by faculty of UCSB, particularly focusing on the fossils of the South Coast and the Channel Islands. Since the 1980s, the collection has been augmented by substantial teaching materials, including vertebrate casts and replicas gathered by Prof. André Wyss and plant materials gathered by Prof. Bruce Tiffney, including Carboniferous peels collected by Profs. Vernon Cheadle and Maynard Moseley.

The Museum of Systematics and Ecology