The Henry Raup Wagner Papers comprise Wagner's personal and professional papers spanning his career as an historian, cartographer and bibliographer from roughly 1915 to 1957, as well as the papers of Wagner's wife and associates created before and after his death. Wagner's papers primarily document his research and writing through his correspondence with other scholars and librarians, notes, published writings, and manuscripts. The collection includes the papers of Wagner's assistant Ruth Fry Axe, who took increasing responsibility for his correspondence as his eyesight began to fail in later life and oversaw Wagner's literary estate and posthumous publications. There is also a small amount of material from Wagner's wife, Blanche Collet Wagner, and his probate lawyer Mabel Clausen regarding the disposition of both Wagner's and his wife's estate. Materials in this collection include address books, financial ledgers, legal documents, correspondence, and writings in manuscript and published form. The collection is arranged into three series: Biographical files, Correspondence, and Writings.

Series I, Biographical files dates from 1927 to 1978 and contains personal, professional and legal documents pertaining to Wagner's life, business activities and estate. This series includes Wagner's address books and financial ledgers, and the death certificates and last wills and testaments of Wagner and his wife. The address books contain the addresses of bookshops and libraries, as well as notes and drafts of letters. The series also contains Wagner obituaries.

Series II, Correspondence dates from 1915 to 1983 and includes professional and personal correspondence. The series is divided into four subseries, arranged chronologically, for each of the principal correspondents: Henry R. Wagner, Blanche Collet Wagner, Mabel Clausen, and Ruth F. Axe.

Subseries 1, Henry R. Wagner dates from 1915 to 1957 and contains correspondence with scholars, librarians and booksellers regarding Wagner's activities as a book collector and researcher, as well as personal correspondence regarding his health, family, finances, and genealogical research. The subseries includes a longstanding correspondence with the bookseller and librarian R. E. Cowan regarding the sale and exchange of books about California's history. For his research of Sir Francis Drake, Wagner consults the John Carter Brown Library, scholars Andrew Rolle and Francis P. Farquhar, and UCLA librarian Lawrence Clark Powell. Notably, this subseries contains correspondence with George Bird Ginnell regarding Wagner and Grinnell's theories concerning the identity of the Padouca Indians referenced in colonial era literature, and Wagner's inquiries to the Smithsonian Institute requesting material about the Padouca. In an October 8, 1952 letter to the bookseller Glen Dawson, Wagner claims that Ginnell plagiarized his work on the Padouca in the latter's article "Who Were the Padouca," published in the American Anthropologist. A copy of the Grinnell's article accompanies Wagner's letter to Dawson. Other scholars with whom Wagner corresponds include naval historian Samuel Eliot Morison, author of several books on Christopher Columbus, and Carl Irving Wheat, an historical cartographer of the American West. Wagner arranges to donate materials to Yale University Library in correspondence with librarian James T. Babb. Personal correspondence includes correspondence with doctors and Wagner's lawyer Mabel Clausen regarding tax returns. Wagner corresponds with a distant relative, William W. Raup, about Raup family lineage. Additional correspondence with Thomas W. Streeter documents the sale of Mrs. Wagner's collection of paintings of headdresses to the Charles W. Bowers Memorial Museum.

Subseries 2, Blanche Collet Wagner dates from 1943 to 1957 and contains correspondence about the sale of Blanche Wagner's collection of headdresses to the Charles W. Bowers Memorial Museum. The bulk of Blanche's correspondence consists of condolences for her husband's death.

Subseries 3, Mabel Clausen dates from 1951 to 1958 and contains the correspondence and assessment of funds for the Wagners' estate.

Subseries 4, Ruth F. Axe dates from 1951 to 1983 and contains correspondence Axe conducted in her capacity as Wagner's assistant and legal guardian. In confidential correspondence with Wagner's friends and associates Francis P. Farquhar and Thomas W. Streeter, Axe keeps them informed of Wagner's health and financial difficulties. Additionally, Axe writes to Wagner's attorney Mabel Clausen about the Wagner family's affairs. The remaining correspondence documents Axe's activities managing the Wagner family estate, Wagner's donations to libraries, and publications.

Series III, Writings dates from 1925 to 1982 and consists of Wagner's publications and manuscripts on Latin and Western American history. The series is divided into two subseries, arranged by materials. From journal articles and historical societies in California, the two subseries are: Articles and Primary source collections.

Subseries 1, Articles dates from 1925 to 1957 and contains mostly published writings and a small amount of manuscript writings.

Subseries 2, Primary source collections dates from 1945 to 1982 and contains documentation of Wagner collections at the Yale, UCLA, Bancroft, and San Diego State libraries. The collections documented in this series include Wagner's publications and primary sources, research files, and unpublished writings.