Various forest types are distributed in headwater streams. However, differences in diatom assemblages among forest types in Japan have not been thoroughly investigated. The objective of this study was to determine differences in diatom assemblages in the most common forest types in Japanese headwater streams, old-growth broadleaf forest (OBF) and planted coniferous forest (PCF) types, and to identify diatom species that tend to grow in either the OBF or PCF forest types. Diatom abundance differed between the forest types, but the numbers of species, genera and families did not. Nonmetric multidimensional scaling analysis revealed the differences in diatom assemblages in OBF and PCF types and this difference was brought by particularly of some genera such as Gomphonema, Planothidium and Navicula. Differences in diatom assemblages between the two forest types were considered to be a reflection of the different environmental conditions such as light condition and alkalinity, created by the different forest types.