Phytoplasmas infect over 200 plant species, prominent examples are coconut, sugarcane, and sandalwood. They are are considered of quarantine relevance e.g. in the EU, which means that their spread is especially tightly regulated. There are no fully resistant crop varieties currently available. Therefore, main disease management strategies are limited to control of the vectors provided that those are known, and the elimination of infected plants. There is a great need for reliable and efficient methods for identification for this group of pathogens, and our standard barcoding regions are likely inefficient.