Bacterial leaf Blight caused by Xanthomonas oryzae pv. oryzae represents a severe threat to rice cultivation in Mali. Characterizing the pathotypic diversity of bacterial populations is key to the management of pathogen-resistant varieties. Forty-one Xanthomonas oryzae pv. oryzae isolates were collected between 2010 and 2013 in the major rice growing regions in Mali. All of them were virulent on the susceptible rice variety Azucena, and their evaluation on twelve near-isogenic rice lines, each carrying a single resistance gene, identified six new races (A4 to A9) and confirmed race A3 that was previously reported in Mali. Races A5 and A6, isolated in Office du Niger and Selingue are the most prevalent ones in Mali. Race A9 is the most virulent, circumventing all the resistance genes tested. Xa3 controlled six out of seven races, i.e. 89% of the isolates tested. The expansion of race A9 represents a major risk to rice cultivation and the urgent need to identify local source of resistance. We selected fourteen isolates of Xanthomonas oryzae pv. oryzae representative of the most prevalent races to evaluate twenty-nine rice varieties grown by farmers in Mali. Six of them showed a high level of resistance to Xanthomonas oryzae pv. oryzae and were then screened with a larger collection of isolates. Based on the interactions among the six varieties and the Xanthomonas oryzae pv. oryzae isolates we characterized eight different pathotypes (P1 to P8). Two rice varieties, SK20-28 and Gigante effectively control all the isolates tested. The low association observed among races and pathotypes of Xanthomonas oryzae pv. oryzae suggests that the resistance observed in the local rice varieties does not simply rely on single known Xa genes. Xanthomonas oryzae pv. oryzae is pathogenically and geographically diverse. Both the races of Xanthomonas oryzae pv. oryzae characterized in this study and the identification of sources of resistance in local rice varieties provide useful information to inform the design of effective breeding programs for resistance to bacterial leaf blight in Mali.