A modified procedure of cDNA-amplified fragment length polymorphism (cDNA-AFLP) combined with silver staining is described which generates clear band patterns from both fungal total RNA and poly-A RNA. The silver staining procedure takes only 25 min. Some 42-55 transcript-derived fragments (TDFs) were yielded from the total RNA of eight fungal pathogens. In comparison with the fingerprints generated from Mycosphaerella graminicola total RNA, those from poly-A RNA showed eight TDFs with an increased intensity and also seven additional TDFs. It suggests that poly-A RNA is preferable as starting material for ideal cDNA-AFLP analysis.