The John Henry Eagleston papers contain materials related to Eagleson's life and time at sea. The majority of the collection is made up of transcripts of his autobiography, Ups and Downs of Captain John Eagleston. This collection has been divided into two series.

Series I. John Henry Eagleston Papers includes ships' papers from the brig Mermaid, which he commanded and a letter that Eagleston wrote to the editor of the Salem Register about the Fiji Islands. Included is the original letter written by Eagleston, the newspaper article, and a photocopy of the article. Other ships' papers, from the bark Edward Koppisch and the brig Mermaid, were removed from their log books and placed with this collection.The majority of papers removed from the log of the Mermaid, are news clippings about weather conditions, tide, local news, and trade prices.This series also includes a transcript of Eagleston's article "Account of An Early California Passage" and transcribed correspondence and ships' papers. There is a folder of transcripts of ship logs.

Series II. Ups and Downs of Captain John Eagleston contains manuscripts and transcripts of the autobiography and correspondence to and from one of Eagleson's sons, James V. Eagleston, to the Essex Institute about the possibility of publishing his father's autobiography. In a letter dated September 27, 1924, it is suggested to Eagleston's son that he have a type-written copy made of his father's autobiography that is found within the ships' logs. This series also contains multiple copies of transcriptions of the autobiography, in loose and bound form, which appear to have been produced by different individuals. The different versions have not been intermingled. The only version whose producer can be identified is the version created by the Lahaina Restoration Foundation in Maui, Hawaii. This version contains the first four chapters, which have been indexed, and are contained within black covers; these transcriptions have been renamed The Journals of Captain John H. Eagleston. For a detailed explanation as to how information about Eagleston and his journals ended up in Hawaii, and why a copy of these transcripts were provided to the Library, see the introduction of the first chapter (box 3, folder 1). It is possible that the first version listed in the finding aid was compiled by Eagleson's son, James V., as it was with his correspondence with the Essex Institute. This autobiography is an excellent resource for descriptions of foreign ports and customs, as seen through an American sailor's eyes.