In a process of selection and breeding over many years, the yield and other agronomically important traits of aromatic and medicinal plants have been greatly improved. Yet, controlling for these important factors and simultaneously preserve high chemical quality, both yield and composition, on the plant and post-harvest, is still a challenging task. In the last few decades plant breeding evolved from classic breeding to molecular breeding using marker assisted selection (MAS). Due to the high prices and labor intense, MAS was limited to major crops such as rice and corn and vegetables such as tomato, pepper and melon. Nowadays, when DNA sequencing is fast, high-throughput, reliable and reasonably priced, MAS can be applied to various crops and plant species. When more and more genomes are being solved, applying state of the art mapping methods to aromatic and medicinal plants is just a matter of time. In conjugation with novel genome editing techniques we try to create modern tools to address scientific questions and breeding needs.