Two basic categories of materials are housed in the archives: institutional records and special collections.

Institutional records include administrative files and reports of former directors; correspondence and professional papers of former museum scientists, curators, and honorary associates; museum publications; scrapbooks of newspaper and magazine clippings; biographical files on former directors, trustees, staff, and students; and memorabilia.

The archives also hold special collections that concern people, events, and research activities associated with the museum. Processed material of this type includes the Raymond M. Gilmore collection on marine mammals (over 65 boxes). There are also several unprocessed collections relating to scientists associated with the museum such as botanists Ethel Bailey Higgins and Reid Moran, herpetologist Laurence Klauber, scientific publisher and collector Charles Orcutt, curator of birds and mammals Laurence Huey, paleontologist and geologist Anthony Wayne Vogdes, and others, along with the records of the Vermillion Sea Station research facility.

Zoologist Raymond M. Gilmore led whale-watching tours for the Museum for 25 years.

Botanist Reid V. Moran collecting plants in Baja California.