| Summary: | <i>Rosa rugosa</i> L. was a famous aromatic plant whose cultivars (<i>Rosa × rugosa)</i> have been widely used in the perfume industry in Asia. The perfume market looks for rose cultivars bearing higher essential oil, while the oil yields of most <i>R. × rugosa</i> have not been evaluated due to limiting conditions, such as insufficient cultivation areas. Here, we tested the yield and the aroma components of essential oil of 19 <i>R. × rugosa.</i> The results indicated that the yields of nerol, citronellol, and geraniol could represent an alternative index of the total yield of essential oil. Sequence syntenic analysis indicated that the <i>Rosa</i> genus specific cis-element Box38 was highly polymorphic. The Box38 region isolation of <i>Rosa × rugosa</i> by flanked primers proved that Box38 repeat number was significantly positively correlated with the essential oil yield of the corresponding cultivar. In the breeding of <i>Rosa × rugosa</i>, six-Box38-repeat could be a robust threshold for selection of high-essential-oil roses. Together, we found that Box38 was a DNA marker for essential oil yield and that it would be helpful in the early selection and breeding of essential oil roses.
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