The Entomology collection consists of approximately 980,000 pinned and labeled insects and 20,000 insects preserved in 70% ethanol. These specimens are used in support of the Museum's mission: "to interpret the natural world through research, education, and exhibits; to promote understanding of the evolution and diversity of Southern California and the peninsula of Baja California; and to inspire in all people respect for the environment." The collection began with a few beetle specimens collected locally in the 1850s, and has been developed since through field collections and donations of significant individual research collections (e.g., 24,000 specimens of the Fred Thorne and William Hedges Lepidoptera collections). The collection contains voucher specimens obtained as the direct result of regional environmental surveys and specimens retained from forensic investigations. The collection is especially strong in Coleoptera (Beetles; 30%) and Lepidoptera (Butterflies/Moths; 30%), with smaller but important holdings of Diptera (Flies; 10%), Hymenoptera (Bees; 10%) and Neuroptera (Lacewings; 5%). The type collection includes over 200 primary types and 500 paratypes with an emphasis on Lepidoptera (butterflies, moths, etc.) and Coleoptera (beetles). There are also 15 holotypes of Arachnids, mostly tarantulas.
Specimens and associated data from the entomology collection are actively incorporated into the public programming functions of the Museum. Specimens are used in exhibits, educational programming, and presented via the website .
The entomology collection is the only such repository in the county, providing a source of distributional data for land use planning research and environmental surveys. With the increasing concern over the impact of growth on the natural environment, this collection reflects the changes due to growth over the last 150 years for San Diego County and 100 years for northwestern Mexico. Many of the species represented in the collection no longer occur in the region, are rare, or have become extinct. Thus the collection is frequently used by the County Dept. of Agriculture, Environmental Health Dept., Medical Examiners Office, US Fish and Wildlife Service and privately-based environmental consultants. Data and applied research reflecting local issues are incorporated into research carried out by researchers studying biodiversity and environmental systems. Professional entomologists worldwide request loans and over 100 researchers consult the collections annually.