Diagnostic of plant diseases is evolving and improving day by day. Molecular-based tools such as real-time PCR, LAMP, microarrays, barcoding and Next Generation Sequencing are enhancing the accuracy of the detection and identification of plant pathogenic bacteria. These technolo­ gies are currently based on the use of available nucleic acid sequences and information about the molecular interactions bacteria! pathogen-plant host. The target DNA sequences selected for these techniques must be distinctive and based on conserved regions, in order to identify only one species, subspecies, pathovar or a particular set of genes. However, the currently available databases contain only a small portian of the sequences of the microbes present in complex environments. The use of integrated approaches for detection and identification of plant pathogenic bacteria has allowed the discovery of differences among strains classified to date in the same species but  showing distinct characteristics in molecular  identification tests.

Three examples are presented: 1) Erwinia piriflorinigrans, a new pathogenic species described in  Spain as causal agent of necrosis of pear blossoms that is closely related to f.  amylovora, 2)   a new Xanthomonas sp., also isolated in Spain and responsible of symptoms similar to those of Xanthomonas arborícola pv. pruni , but classified as different to this species according to multi­ locus sequencing analysis as well as to serological and PCR identification, 3) the new group of Pseudomonas syringae pv. actinidiae strains described from New Zealand, France and Spain, that show  low  virulence  and  different  molecular  characteristics. The description  of  new species or infra-specific groups leads to a more comprehensive knowledge of the complex pathosys­ tems in agricultura! industry and nature. Moreover, the partial or complete genomes of new taxons that are being determined will offer new omics-based tools for improving the detection, identification and taxonomy of bacteria! plant pathogens.