'so-yeop' in Korean, and 'Jiso' in Japanese) [1; 2; 3]. Its recognized bioactivities include antioxidant [4; 5], anti-allergic [6; 7; 8], anti-inflammatory [6; 7; 8; 9], antipruritic [9], and anti-HIV-1 [10] activity. It is also a common ingredient in foods such as pickles ('Shiso' in Japanese), with two different leaf colors caused by their differing accumulation of anthocyanins [11; 12; 13]: a red-purple type (red perilla, _P. frutescens_ var. _acuta_ (Odash.) [PERSON] and _crispa_ (Benth.) [PERSON], Jasoyeop in Korean, Aka-jiso in Japanese) and a green-purple type (green perilla, _P. frutescens_ f. _viridis_ Makino, 'Chungsoyeop' in Korean, 'Ao-jiso' in Japanese). Perilla varieties are commonly classified into seven chemo-types based on their varying quantities of the main components of its essential oil, perillaldehyde (PA), perilla ketone (PK), elsholtzia ketone (EK), citral (C), perillene (PL), piperitone (PT), and phenylpropanol (PP) [14; 15]. In Korea, the Perilla genus has been classified into two major chemo-types, PA (soyeop) and PK (Dlggae), according to the main components of their volatile oils. PA plants contain mostly perillaldehyde (19.8%) and limonene (57.7%), while the oil of PK plants is mainly perilla ketone (89.8%) [16]. The leaves and seeds of PK plants have traditionally been used as food, whereas the leaves and twigs of PA plants are used in herbal medicine. Recently, Korean perilla breeders have developed new and improved perilla varieties with high yield and nutritional quality by crossing between subspecies. These diverse varieties of PA and PK perilla are difficult to distinguish morphologically, and the accurate and rapid identification of these varieties using the nuclear ribosomal internal transcribed spacer (ITS) region or chloroplast DNA regions (matK, psbA-trnH, and trnL-trnF) is limited by the relatedness of the subspecies (Table S1). If they should be used in herbal medicine and as a health food supplement, the development of accurate methods for the identification and characterization of these varieties at the subspecies level is required. Previous studies have reported genetic differences between cultivated and woody forms of perilla using random amplified polymorphic DNA and amplified fragment length polymorphism markers; however, the accuracy of these analyses is limited by population dynamics and their reproducibility as the diagnostic markers of perilla in the field [1; 2]. Recent advances in next-generation sequencing and RNA sequencing have provided not only a fast, cost-effective, and reliable approach to generate large datasets for functional genomic and transcriptomic analysis, but also more comprehensive and efficient means to quantify specific expression patterns between subspecies. These new techniques have been applied to red and green perilla varieties, yielding useful information for transcript discovery, and expression profiling, highlighting differences between the two genotypes [17; 18; 19]. In the present study, we referred to data for the transcriptomic differences identified between the red and green PA perilla varieties [17; 18] to select putative informative genes and establish simple sequence repeat (SSR) and insertion-deletion (indel) markers to enable breeders to readily distinguish between perilla varieties. SSR markers have been widely used as genetic markers, which are very useful for a spectrum of genetic and breeding applications because of their abundance, reproducibility, high level of polymorphism, co-dominance inheritance, and easy detection by PCR [20; 21]. We selected three candidate genes, _LS, Myb-P1_, and _DFR_, among the identified differentially expressed genes for perilla plants that feature red and green forms of anthocyanin accumulation from RNA-seq data [17; 18].