The Thomas C. Dudley papers contain five journals kept by Dudley during his time in the United States Navy. Some of the journals have loose pieces of paper or page markers in them. The first journal, which covers the first half of 1853, begins at Norfolk, Virginia, and follows the frigate USS Powhatan to the Bay of Cuni-sing-moon near Hong Kong. The second journal spans from September 1853 to October 1854. What is interesting about this second journal is that it was bound as a journal, from letters that Dudley sent to himself in the states, after he returned home from the expedition. This was done as a way for Dudley to get around Perry's General Order Number One, which required all notes, journals, and drawings to be kept or collected by the squadron and sent to the Navy Department in the states. It is possible that the subsequent journals were assembled in the same fashion; however, this is the only journal in which Dudley mentions this method. There is a postscript at the end of this journal dated 1925, referring to the death of an unidentified Japanese man. The third journal begins in October 1854 and ends December 1855; sailing from the Yellow Sea to Cape Town, South Africa.

The fourth journal was kept simultaneously as the second and third journals, and is a journal in the form of a newspaper. Calling it the The Japan Gazette, Dudley "edited and published" this newspaper in 1854; it is unclear if this paper was actually published. The Japan Gazette includes illustrations and news items. Included with in the pages of the volume was a loose manuscript describing an onshore excursion; this has been removed from the volume but placed within the same folder.

The fifth journal begins January 1, 1856 and ends December 31, 1856. It follows the frigate USS Powhatan from Cape Town, South Africa back to Norfolk, Virginia. In it, Dudley journals his travels from Norfolk back to his home in New York City. It should be noted that this volume appears to have been rebound, and that the canvas cover sewn on to it appears to be from one of Dudley's other journals (particularly volume 3), as it says October 12, 1854 on it.