Xanthomonas albilineans is a xylem-invading pathogen that causes leaf scald, one of the major diseases of sugarcane. Interestingly, this pathogen lacks both the xanthan gum genes cluster and a type III secretion system (T3SS) of the Hrp1 and Hrp2 injectisome families (1). X. albilineans produces a unique and specific toxin, albicidin, which is a powerful DNA gyrase inhibitor. Consequently, albicidin blocks chloroplasts differentiation, resulting in leaf scald symptoms. High genetic and pathogenic variability exists among strains of X. albilineans, and 10 genetic groups were identified by pulsed field gel electrophoresis (PFGE). All strains involved in sugarcane leaf scald disease outbreaks since the late 1980s belong to the same genetic group called PFGE-B, whereas the strains isolated previously belong to other groups, especially to group PFGE-A. These two groups were also revealed by multilocus sequence analysis (MLSA) using seven housekeeping genes (groEL, dnaK, gyrB, atpD, efp, recA and glnA). The complete genome sequence of strain GPE PC73 belonging to PFGE-B is now available (1). To better understand the genetic differences between the PFGE-A and PFGE-B strains, Suppression Subtractive Hybridization (SSH) analysis was performed to compare the genomes of XaFL07-1 (PFGE-B) and Xa23R1 (PFGE-A), both isolated in Florida. SSH is a method used to identify DNA fragments that are uniquely found in one strain when compared with another, closely related bacterial strain (2,3). We enriched a library of unique DNA sequences from strain XaFL07-1 (tester strain), using Xa23R1 DNA as the driver strain. A total of 188 XaFL07-1-specific clones were generated and sequenced. Sequences were all compared against the GPE PC73 genome and against the GenBank non redundant database (NCBI). Initial screening focused on 12 genes with potential pathogenicity function and for which SSH data were confirmed by PCR and Southern blot hybridization. These included a DNA methyltransferase, a ch