Particularly notable among manuscript collections for the early history of San Diego are the papers of Ephraim W. Morse and his family. A pioneer settler, merchant, and civic leader active in the early development of the city, the Morse correspondence, business records, notebooks, and photographs document life in the region in the late 19th and early 20th centuries. The archives of Ed Fletcher, a prominent San Diego businessman, land developer, civic leader, and State Senator, provide extensive documentation on the development of Southern California water, highway, and urban development. Settlement and business development in the west can also be researched in the Dawson Family Papers, in which correspondence, diaries, scrapbooks, and photographs document a highly successful cattle operation with ranches in Texas, New Mexico, and Colorado. Many of the manuscript collections provide not only information on the growth of the region but also insight into a particular time and place
Contemporary issues and political activism are also documented through the manuscript collections. The papers of Chicano activist and political organizer Herman Baca include extensive files on Chicano issues, organizations, individuals, and activities in the San Diego and the Mexican border region, as well as photographs documenting people and events. The United States-Mexico Border Program Records of the American Friends Service Committee describes human rights advocacy in the area, specifically the San Diego County - Mexico border. The main components of the records are abuse complaint files and legal case documents generated by citizens and immigrants in the years 1977-2000. The Ben Yellen Papers record the struggle for civil rights for farmworkers, both domestic and migrant, in the Imperial Valley. On a separate political front, the August S. Carstens Collection consists of materials relating to the movement opposing the construction and operation of nuclear power plants in California. The papers of San Diego journalists Neil Morgan, Lee Shippey, and Gerald Warren record the political and cultural issues of the city and region.
Printed books, directories, pamphlets, ephemera, promotional publications, newspapers, maps, and photographs provide additional context for the regional manuscript collections. Including but also extending beyond Southern California, the Jessie H. and John B. Goodman Collection includes extensive holdings on the Gold Rush, overland narratives, directories, and the later development of the state. The Hill Collection of Pacific Voyages, the preeminent collection of pre-1850 voyages of exploration and discovery to the Pacific, includes printed accounts of expeditions and travels to Alaska, California, and the Pacific Northwest; the holdings include first editions of the Lewis and Clark Expedition, Zebulon Pike, and explorations of the Northwest Passage. The Richard and Naomi Lingenfelter Western Mining Collection is an exhaustive gathering of works on all aspects of mining in the Western United States.