Information on seed morphology and fruiting phenology related to fitness and reproductive strategy is important for plant ecology and evolution. Although seed morphology is highly variable across years, regions and mother trees even within the same species, seed mass and size are often reported as averages or ranges for each species in existing databases or picture books. Unfortunately, freely available seed trait data for individual seeds are limited. This paper reports data on morphology (seed length, width and height) and dry weight of individual seeds from 129 tree species in Japan. It includes data from 79 genera in 44 families collected from various forests located in cool temperate to subtropical regions in Japan, including species not reported in previous databases. We mainly used seeds from the collections of the Forest Tree Gene Bank Program, but new seeds were also collected. If possible, multiple seeds were collected from multiple mother trees of the same species. This paper also reports data of the sampling month and date, which indicates the fruiting season of trees at the sampling site. By comparing these data to past or future data, we hope that it will aid in understanding the effects of climate change on fruiting phenology. The complete data set for this abstract published in the Data Paper section of the journal is available in electronic format in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2020-14.1/jalter-en.
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