Subseries A. Japan offers documentation of the years Morse resided in Japan as Professor of Zoology at the Imperial University of Tokyo, and his 1882 ethnological expedition funded by the Trustees of the Peabody Museum of Salem. Documentation of his university tenure is sparse. Included are student papers and his teaching contract. Morse's sketches and notes reflect his eclectic curiosity. They include examples of shop signs, fireworks, hairpins, agricultural tools, and views of Noritane Ninegawa's studio.

Morse's numerous interests are revealed in the materials he collected. He perceived the exigency of documenting life in Japan before it was transformed by western modernization. Included are tea ceremony records, genealogies, and architectural drawings. Much of the series is written in Japanese.