This paper discusses the origins of papers of Japanese historical materials focusing on paper composition and mixtures. Many preliminary studies on palaeography, history, and the scientific studies of cultural properties have mentioned fibre components and tried to identify the paper types and quality. Historical materials require non-destructive surveys, and no botanical or mineralogical analyses of the paper composition have ever been conducted or emphasised. In the core research project of the National Museum of Japanese History, ‘Integrated Studies of Cultural and Research Resources’, Japanese historical papers were examined through detailed microscopic observations using a high-precision digital microscope. Differences in the conditions of surfaces and fibre arrangements showed different paper materials, and the quantity and density of the mixtures such as fibres, plant tissues, starch grains, and minerals may have been created by paper-making techniques or historical conservation processes. The taxonomic identification of paper mixtures enables the reconstruction of the origins of papers, which can lead to interpreting the historical and environmental backgrounds of documents such as economic changes and social transitions.