In conjunction with the emergence of Xylella fastidiosa (Xf) in Europe, several interceptions of coffee plants contaminated with Xf occurred in France. Different XF subspecies and sequence-types (ST) were identified: fastidiosa (ST75), sandyi (ST72 and ST76) and pauca (ST53 and ST74). Since the discovery of a focus of Polygala myrtifolia (Pm) in natural settings in 2015 in Corsica and the French Riviera, this pathogen has been detected on thirty plant species with a validated method based on real time PCR (Harper et al, 2010) associated with a DNA extraction kit (BioNobile). Characterization of isolates directly on plants, or for strains isolated on modified PWG medium is performed according to multilocus sequence typing (MLST) (http://ubmlst.org/xfastidiosa/). Following EPPO protocol PM 7/24, isolates were mostly allocated to sequence types ST6 and ST7 (subspecies multiplex). Mixed infection by ST6 and ST7 was demonstrated by isolation of both strains from one Pm. Modifications to a proposed amplification protocol revealed infections linked to the subspecies pauca, sandyi, one recombinant and some mixed infections. The EPPO protocol MLST confirmed identification of four Pm contaminated with subsp pauca but not the identification of other contaminants. These contaminations were not observed again in the immediate environment after plant eradication. Subspecies assignation directly from plant material is not always successfully linked to PCR inhibitors depending of host plants. This study confirms the diversity of subspecies of Xf in France, but the subspecies multiplex was found to greatly predominate..