The use of control measures for the circulation of plant material is an essential tool to avoid the introduction of pathogens into new areas, where they could have devastating effects. However, these control measures face multiple technical limitations (imposed by the protocols used) and practical limitations (the need to trade plant material) which can make it difficult to achieve the necessary levels of environmental protection against new pathogens. The project aims to develop sensitive, accurate, rapid, and repeatable protocols that use Next Generation Sequencing (NGS) technologies for the detection of quarantine pathogens in imported plants. First of all, the project intends to build a solid protocol using numerous experimental samples containing nucleic acids extracted from different organs of healthy plants, mixed with the DNA of quarantine pathogens of fungal or bacterial nature (such as Phytophthora ramosum or Xylella fastidiosa), so to evaluate the sensitivity, accuracy, and repeatability of the analyzes carried out with the nanopore sequencers of a portion of the 16S rRNA gene (for bacteria) or ITS (for fungi) in order to obtain an identification of the species in the field and in a few hours.