Series II. Diaries covers the years 1856-1913, and includes travel diaries from Japan and Europe. All the diaries are extensively illustrated.

The journal which he kept from 1856 to 1863 provides an excellent record of Morse’s years as a student and assistant to Louis Agassiz. Of interest are humorous sketches of members of the "Agassiz Zoological Club," an informal organization formed by Morse and his fellow students. In his entry of January 1, 1860, Morse notes his academic improvements over the past year and dedicates the remainder of his life to the pursuit of scientific knowledge. The displacement of Japan’s feudal culture by western modernization is documented in the journal kept by Morse during his 1882 ethnological expedition to the Orient. His copious notes and abundant sketches were used to produce books on Japanese architecture and customs, the most notable being his 1917 publication Japan Day by Day.