Aster savatieri (2n=2x=18) is distributed in Honshu, Shikoku, and Kyushu, Japan. Dwarf forms of A. savatieri growing on serpentine soils (in Aichi and Mie prefectures, and Shikoku) are recognized as A. savatieri var. pygmaeus. Serpentine soils are characterized by low nutrient levels (e.g., nitrogen, phosphorus, and potassium), low calcium/magnesium ratios, and high heavy-metal contents. These soil conditions generally have negative effects on plant growth, and plants endemic to serpentine soils are thought to be adapted to the soil conditions. This RNA-seq analysis was performed to generate transcriptome databases, which will be used to develop simple sequence repeat (SSR) markers to reveal the genetic diversity and population structure of different populations of A. savatieri and A. savatieri var. pygmaeus.