Abstract: Stemphylium vesicarium, is the causal agent of brown spot of pear, a fungal diseasethat produces important economical losses in pear growing areas of European countries. Besidesthe pathogenicity on pear the fungus is able to grow saprophytically on dead plant material in theorchard. The quantification of inoculum in the orchard is required for the application ofintegrated disease control measures. The assessment of the inoculum is performed through aerialspore traps. However, not all the spores trapped are pathogenic. Therefore, the characterization ofthe populations of the fungus on the basis of their saprophytic-pathogenic profile is required todefine more efficient disease management strategies. Accordingly, the pathogenicity on pear of125 isolates of S. vesicarium obtained from different sources (air, lesions, leaf plant debris, andnon host plants) in Northeastern Spanish pear orchards was determined. Representative isolateswere characterized at molecular level with RAPD and AFLPs techniques. Several RAPD andAFLPs fragments were selected to design a duplex PCR specific for S. vesicarium and for pearpathogenic isolates.