Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR associated sequences (cas) form hypervariable loci which are widely distributed in prokaryotes. The repetitive region is characterized by short interspersed unique spacer sequences which often match to bacteriophage-derived DNA, thus providing immunity against foreign genetic elements, in particular bacteriophages. Bacteria of the genus Xanthomonas cause diseases on over 400 different host plants, including many economically important crops, such as rice, wheat, citrus, and banana plants. We screened more than 300 strains of Xanthomonas, representing ten different species (44 pathovars), for the presence of CRISPR loci. Only a few pathovars were found to possess a CRISPR locus, among them X. axonopodis pv. vasculorum, X. axonopodis pv. cassavae, X. campestris pv. raphani, X. citri pv. citri, X. oryzae pv. oryzae (Xoo), X. translucens, and X vasicola pv. musacearum. Presence/absence of CRISPR loci appeared to be conserved at the pathovar level, except for Xoo. The apparent absence of CRISPR loci from African Xoo isolates confirms previous results showing that African Xoo isolates form a phylogenetic group that is distant from the Asian Xoo group. Comparative genomics suggested that the common ancestor of all xanthomonads had two CRISPR loci which in most species/pathovars got lost during evolution. Based on DNA sequence information about the terminal spacers of 32 Asian Xoo CRISPR loci we postulate that the common ancestor of these strains had all the spacers which are nowadays still found in a few strains and that some spacers got lost during evolution in some Xoo lineages. This work represents the first proof of concept of CRISPR analysis as a molecular tool for high-resolution strain typing, phylogenetic studies, and global surveillance of a phytopathogen. (Texte intégral)