| Summary: | <i>Primula</i> comprises many species of horticultural value. In Korea, six species grow in the wild. Yamazaki classified the variety <i>Primula modesta</i> var. <i>fauriei</i> into <i>P. modesta</i> var. <i>hannasanensis</i> and <i>P. modesta</i> var. <i>koreana</i> based on the differences in leaf morphology. We compared the chloroplast genome sequences of the two Korean endemic <i>Primula</i> varieties and found that both had the typical quadripartite structure of angiosperms. The chloroplast genome size of <i>P. modesta</i> var. <i>hannasanensis</i> is 154,772 bp, including an 85,238 bp large single-copy region and a 17,790 bp small single-copy region, whereas that of <i>P. modesta</i> var. <i>koreana</i> is 154,667 bp, including an 85,152 bp large single-copy region and a 17,771 bp small single-copy region. The inverted repeat region is 25,872 bp in both varieties. We predicted 129 genes—84 protein-coding genes, 8 rRNAs, and 37 tRNAs. We identified 536 single-nucleotide polymorphisms and 501 indels between the varieties. Phylogenetic analysis revealed that the two varieties formed a sister group in the clade <i>P. knuthiana</i>–<i>P. stenocalyx</i>. This study will contribute to phylogenetic, taxonomic, and evolutionary studies of the genus <i>Primula</i>; it will also contribute to the analysis of the genetic diversity of the two varieties, and to the development of identification markers.
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