Cultivation of medicinal and aromatic plants (MAP) today is not only a promising alternative and counterpoint to wild collection, enabling preservation of natural genetic variability and survival of rare, endemic, vulnerable and endangered species, but also represents a powerful economy branch providing the high class quality raw material for pharmaceutical, cosmetic and the food industry. Domestication and cultivation of most of medicinal plants, usually conceived as a minor crops, face with many challenges on small, medium and large scale production, relating both cultivation technologies and market and prices fluctuations. Cultivated MAP material is increasingly preferred by the herbal industry, because it is easier to predict plant yield, quality and drug composition, especially when compared with wild harvested raw materials. In case of cultivated MAP material, the possibility of plant misidentification and adulteration is excluded. The profitability of cultivation of medicinal plants compete with profit achievable for standard field crops for which already exist a specialized machinery and a standard procedure for application of fertilizers and agrochemicals to control weeds, pests and diseases. For successful large scale cultivation of MAP, the high quality raw material should be produced using low input cultivation methods to be competitive at the international market and with plants collected from the wild. The most common issues with which the producers of medicinal plants encountered are the market, abundance and accessibility of wild populations, agro-environmental conditions, labor availability and costs, investments in machinery, post-harvest processing, and profitability of production. Superior genotypes are very important for profitable production of the high quality medicinal plants' row material. Out of all cultivated medicinal plant species, only a small percentage is clearly genetically defined and represented on the seed market in term of variety. Similarly to the other crops, traditional breeding methods, as well as biotechnological procedures and selection assisted by molecular markers are applied in development of new varieties and Mapping of genes and specific DNA sequences involved in biosynthesis of particular metabolite classes seems to be a future challenge in MAP breeding programs. Most of actual research is focused on genetic variability among different taxa of medicinal plants using several types of DNA markers, including restriction fragment length polymorphism (RFLP), amplified fragment length polymorphic DNA (AFLP), random amplified polymorphic DNA (RAPD), cleavage amplified polymorphic sequence (CAPS), simple sequence repeat (SSR), and sequence characterized amplified region (SCAR) markers. Although the primary target for trait manipulation in medicinal plants is the content of active compounds, for development as crops, basic agronomic characters related to uniformity, stability, growth and development, and resistance to biotic and abiotic stresses, must also be impro...