The phylogenetic relationships of Xylella fastidiosa strains isolated from different hosts, including citrus trees, coffee, grapevine, plum and pear, were inferred by sequence analysis of the 16S rDNA and 16S-23S intergenic spacer region. A high level of similarity (97.1-100%) was found in the 16S rDNA of the Xylella fastidiosa strains. The 16S-23S region showed a higher level of variation, with similarity values ranging from 79.8 to 100%. Two tRNAs (tRNA(Ala) and tRNA(Ile)) were encountered within the spacer sequence. The phylogenetic trees, constructed using the neighbour-joining method, showed that the citrus, coffee, peach and plum strains were closely related and separate from grapevine strains. The pear strain remained isolated from all the other Xylella strains in both analyses and produced values of less than 20% in DNA-DNA hybridization experiments with a citrus strain. These results show that this strain does not belong to the Xylella fastidiosa genomic species.