MultiLocus Variable number of tandem repeat Analysis (MLVA) has been extensively used to examine epidemiological and evolutionary issues on monomorphic human pathogenic bacteria. MLVA is gaining popularity on agriculturally important bacterial plant pathogens as a tool to improve our understanding of their epidemiology. Xanthomonas citri pv. citri, the causal agent of Asiatic citrus canker, is a quarantine organism in several countries and a major threat for the citrus industry worldwide. We screened the genomes of X. citri pv. citri strain IAPAR 306 and of phylogenetically related strains for tandem repeats. Two MLVA schemes targeting minisatellites and microsatellites, respectively, were developed to assess the diversity of this monomorphic bacterium at various spatio-temporal scales. Microsatellites are useful for outbreak investigation. In contrast, minisatellites were used to decipher the global diversity of X. citri pv. citri and revealed four pathotype-specific lineages based on Discriminant Analysis of Principal Components (DAPC). A single lineage (DAPC1) comprised strains that were implicated in the major geographical expansion of X. citri pv. citri during the 20th century. When applied to the analysis of the emergence of in Africa, minisatellites revealed the presence of two different genetic lineages in addition to DAPC1 on this continent, consistent with SNP data derived from draft genome sequences. Using bacterial populations collected in two neighboring Western African countries, Mali and Burkina Faso, we applied these two genotyping schemes to investigate the origin and pathways of these emergences. Minisatellite and SNP data suggested the introduction of two groups of strains in Mali (DAPC1 and DAPC2). DAPC2 was restricted to Bamako district, whereas DAPC1 strains were found much more invasive. The latter strains formed a major clonal complex based on microsatellite data. This suggests that human activities played a major role in the spread of DAPC1