The Ebenezer B. Crocker papers are made up of shipping papers from Crocker's time as a supercargo; they contain material from vessels that Crocker worked on and account books that belonged to Crocker. This collection is divided into two series.

Series I. Ships' Papers contains the papers from individual ships and includes bills, invoices, letters of instruction from the ship owners, memoranda, correspondence, and customs duties. It is unclear how the letter of instructions for the ship North America came to be in this collection, as Crocker was neither the owner nor the supercargo of the ship.

Series II. Account books contains fourteen account books focused on individual ships, and on more general accounts. The number assigned to the account books in 1923 has been included in the content list. This series has been divided into two subseries. Subseries A. Ships' Account Books contains account books specific to individual ships. The account book for the ship Massasoit, which contains receipts for cargo brought on board in 1841, has Henry H. Crocker's name on it, but was used by Ebenezer B. Crocker. Subseries B. General Account Books contains account books not specific to one ship.