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<i>Chrysanthemum</i><i>morifolium</i> Ramat. ‘Daboju’ is a <i>C. morifolium</i> cultivar with important ornamental and medicinal values, and is often used in the treatment of colds, blurred vision, dizziness, and itchy skin. As the morphological characteristics of <i>C. morifolium</i> ‘Daboju’ are very similar to those of other <i>C. morifolium</i> cultivars, they are often confused in practice. However, the medicinal value and practical use of <i>C. morifolium</i> depends on using the correct rapid and accurate identification of <i>C. morifolium</i> ‘Daboju’ and its differentiation from other, morphologically similar C. × morifolium cultivars. Twenty-one polymorphic start codon-targeted (SCoT) primers were amplified in 21 distinct <i>C. morifolium</i> cultivars. One cultivar-specific DNA marker was developed with the aim of the rapid and accurate identification of <i>C. morifolium</i> ‘Daboju’ and its differentiation from other, similar <i>C. morifolium</i> cultivars. Twenty-one polymorphic start codon-targeted (SCoT) primers were amplified in 21 distinct <i>C. morifolium</i> cultivars. One cultivar-specific 385-bp amplicon (named SCoT36-385), amplified only in <i>C. morifolium</i> ‘Daboju’ (and in all samples of this cultivar), was identified, cloned, and sequenced. Subsequently, a sequence-characterized amplified region (SCAR) marker (named DBJF/DBJR), generating a 360-bp amplicon, was developed from SCoT36-385 and tested for amplification in all 21 <i>C. morifolium</i> cultivars, ten <i>C. morifolium</i> ‘Daboju’ populations, and different simulated adulterations of ‘Daboju’ with other cultivars. The primers amplified the specific 360-bp-long DNA fragment in all the tested <i>C. morifolium</i> ‘Daboju’ samples but failed in the absence of ‘Daboju’. The detection limit of the SCAR primer pair (DBJF/DBJR) was 100 pg of DNA extracted from <i>C. morifolium</i> ‘Daboju’. Hence, this SCAR marker has a very high detection sensitivity, and can be used for accurate and rapid identification of <i>C. morifolium</i> ‘Daboju’. It can play an important role in ensuring the quality of medicinal preparations and protecting <i>C. morifolium</i> ‘Daboju’ germplasm resources in breeding programs and in identifying lines generated from this cultivar.