Among numerous molecular methodologies developed for highly specific identification of filamentous fungi isolates, here we describe restriction digestion analysis of the ITS products as an easy method to identify isolates of filamentous fungi. This technique is a rapid and reliable method appropriate for routine identification of filamentous fungi. This can be used to screen large numbers of isolates from various environments in a short time. The use of different endonucleases allowed generating individual restriction profiles. The individual profiles obtained were combined into composite restriction patterns characteristic of a species. Eleven different genera can be differentiated and among them 41 different species.