The common bacterial blight, caused by Xanthomonas axonopodis pv. phaseoli (Xap) and X. fuscans subsp. fuscans (Xff), is one of the most important dry bean diseases of bacterial etiology. The present work aimed to study the genetic structure among and within populations, and also identify the pathogenic variability of Xap and Xff isolates evaluating the horizontal and vertical resistance of the host. A total of 42 Xap and Xff isolates were obtained were submitted to molecular characterization by rep-PCR markers, and inoculated in the genotypes CNFP 10120, BRS Notável, and Rosinha G-2, for differential interaction studies. In the analysis of genetic structure, the coefficient of genetic differentiation (GST=0.5154) revealed diversity both within and among the pathogenic populations, confirming the result obtained by AMOVA (FST=0.5198). Of a total of 51 loci, 98% were polymorphic, among Xap 59% and within Xff only 21% were polymorphic. In studies of pathogenic variability, diallelic analyses showed significant effects of the general combination ability (GCA), of the general aggression ability (GAA), and of the specific interaction ability (SIA). Therefore, seven races were classified through the differential behavior of all isolates in the three genotypes of bean.