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<i>Aster spathulifolius</i>, a common ornamental and medicinal plant, is widely distributed in Korea and Japan, and is genetically classified into mainland and island types. Here, we sequenced the whole chloroplast genome of mainland <i>A. spathulifolius</i> and compared it with those of the island type and other <i>Aster</i> species. The chloroplast genome of mainland <i>A. spathulifolius</i> is 152,732 bp with a conserved quadripartite structure, has 37.28% guanine-cytosine (GC) content, and contains 114 non-redundant genes. Comparison of the chloroplast genomes between the two <i>A. spathulifolius</i> lines and the other <i>Aster</i> species revealed that their sequences, GC contents, gene contents and orders, and exon-intron structure were well conserved; however, differences were observed in their lengths, repeat sequences, and the contraction and expansion of the inverted repeats. The variations were mostly in the single-copy regions and non-coding regions, which, together with the detected simple sequence repeats, could be used for the development of molecular markers to distinguish between these plants. All <i>Aster</i> species clustered into a monophyletic group, but the chloroplast genome of mainland <i>A. spathulifolius</i> was more similar to the other <i>Aster</i> species than to that of the island <i>A. spathulifolius</i>. The <i>accD</i> and <i>ndhF</i> genes were detected to be under positive selection within the <i>Aster</i> lineage compared to other related taxa. The complete chloroplast genome of mainland <i>A. spathulifolius</i> presented in this study will be helpful for species identification and the analysis of the genetic diversity, evolution, and phylogenetic relationships in the <i>Aster</i> genus and the Asteraceae.