Non radioactive Differential Display Reverse Transcription- PCR (DDRT-PCR) was used to screen molecular variants at expression level in Pyrenophora graminea and Pyrenophora teres, grown in vitro with glucose or plant cell walls as carbon sources. Several differential transcripts from both species were identified, either constitutive or induced by barley leaf cell walls. Three cloned species-specific transcripts were sequenced: one was constitutively expressed in P. graminea and absent in P. teres, two were specifically induced by host leaf cell walls either in P. graminea or in P. teres. For all three, sequence analysis showed significant homology with known pathogenicity-related genes available in databases, coding for toxic metabolites, cell wall degrading enzymes and regulative factors as kinases. These data are discussed in relation to the biology of the two pathogens under study.