This paper describes the flora of habitat-forming seaweeds (fucoids and temperate kelps) at 7,673 sites of the Japanese coast encompassing its warm to cold temperate zone, recorded from 1887 to 2014. The data set includes 86 species (21,168 presence and 20,845 absence records), compiled from 355 literature sources, most of which were written in Japanese and published as grey literature in local journals or individual reports. Scientific names were consolidated under currently-accepted nomenclature based on Algaebase (http://www.algaebase.org). The data set compiled the seaweed flora at each study site each year, the geographical location and the scientific names. Additionally, three supporting data sets were created respectively including name of each site, synonyms of the seaweeds, and the corresponding literature list. This rich collection of data can be used to study the biogeography and long-term changes of particular species and the diversity of habitat-forming seaweeds of the Japanese coast.