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The quarantine bacterium Xylella fastidiosa has recently emerged as a serious threat to the European and Mediterranean agriculture and landscape, with several outbreaks detected in Italy, France, and Spain. The first finding of the bacterium in Spain occurred in 2016, when cherry (Prunus avium) and Polygala myrtifolia plants were reported to be infected by strains of X. fastidiosa subsp. fastidiosa ST1 and of X. fastidiosa subsp. multiplex ST7 and 81. Since then, numerous outbreaks of the bacterium have been reported in the major Balearic Islands (Mallorca, Menorca, and Ibiza), where more than 15 host species have been found to be infected by different subspecies and STs of X. fastidiosa, including the subspecies pauca ST80 in Ibiza. Later on in 2017, X. fastidiosa subsp. multiplex ST6 was detected for the first time in the mainland Spain, on almond trees in Alicante province (Valencian Community). Draft genome sequences of two X. fastidiosa subsp. multiplex ST6 strains ESVL and IVIA5901 from almond in Alicante, and a X. fastidiosa subsp. fastidiosa ST1 strain IVIA5235, from a cherry tree in Mallorca, were obtained by high throughput WGS using a HiSeq4000 Illumina platform. Pairwise comparisons of the chromosomal genomes of the two X. fastidiosa subsp. multiplex strains showed an average nucleotide identity higher than 99%. Interestingly, the two strains differ for the presence of the plasmids pXF64-Hb_ESVL and pUCLA-ESVL detected only in the ESVL strain. In the case of X. fastidiosa subsp. fastidiosa strain a plasmid, named pXFAS_5235 showing high sequence similarity with the conjugative plasmid pXFAS01 which was reported in X. fastidiosa subsp. fastidiosa strain M23 from almond, was also identified. To confirm the presence/absence of the different plasmids PCR tests were carried out on different cultured strains, and on several infected plant samples collected in the almond orchards in Alicante and in a collection of several host from Balearic Islands. PCR results confirmed the WGS data, and disclosed the occurrence of strains of X. fastidiosa subsp. multiplex ST6 infecting almond trees harboring the two plasmids, only plasmid pUCLA-ESVL or none. Additionally, the presence of plasmid pXFAS_5235 was demonstrated in all host infected by X. fastidiosa subsp. fastidiosa ST1 in Mallorca. The availability of these draft genomes will contribute to extend the European genomic sequence dataset, a first step toward setting new research to elucidate the pathway of introduction and spread of the numerous strains of this subspecies so far detected in Europe.