Correspondence 1855-1946: These letters are arranged chronologically and pertain to Hughes's research into historical topics as well as his personal correspondence. The materials contain information about biographical details and other factual information. These letters provide insight into Hughes's research for the History of the Welsh in Minnesota and Mankato: Its First Fifty Years, Dakota and Winnebago Indians, Traverse des Sioux, and the discovery of some Mayer sketches. Letters written between 1930 and 1934 are primarily of a personal nature.

Research Notes: This section contains research notes used by Hughes for writing books and articles. The notes pertain to research detailing the following publications: Blue Earth County, Indian Chiefs of Southern Minnesota, Semi-Centennial of Mankato, Old Traverse des Sioux, and Welsh in Minnesota. A portion of the materials illustrate Hughes's research into the Sioux Uprising, Spirit Lake Massacre, Steamboating on the Minnesota River, Cambria Mounds, Early Missions in America, Forts Judson, L'Huillier, and Ridgley, Long's Expedition, Mankato Hanging, Minneopa State Park, Minnesota History, Reminiscences, and Roads. Furthermore, the section contains personal biographies not included in Welsh in Minnesota.

Manuscript Drafts: These drafts are for the following research endeavors: "Early History of Mankato and Vicinity," "Early Missions in America," "Fort Ridgley," "Mankato Hanging," "Steamboating on the Minnesota River," "The County Discovered," "The Settlement of Mankato," "The Treaty of Traverse des Sioux," and an untitled paper about Mankato. This section also contains information about Hughes's published research. Manuscripts included are: History of Blue Earth County, Indian Chiefs of Southern Minnesota, Minneopa State Park, Old Traverse des Sioux, and Welsh in Minnesota.

Miscellaneous: This part of the collection contains a variety of information. Topics range from Indian archeology, Hughes legal notes, Legal papers for Patterson v. Shaubhut, newspaper clippings of "Little Journeys Through Early Minnesota History," newspaper clippings for the Mankato Daily Free Press and The Review, notes of public addresses given by Hughes, speeches by E. Raymond Hughes, a travel account, dozens of photographs of American Indians, periodical literature, and information about an Old Settlers' Reunion in 1902.

Volumes: This section contains 69 notebooks with research notes regarding various papers and books written by Hughes. Additionally, certain notebooks contain biographies, reminiscences, a compilation of Mankato area men who participated in World War One, notes from the diary of Andrew Friend, and preliminary drafts of the History of Blue Earth County.