The polymerase chain reaction (PCR) was used to amplify ribosomal internal transcribed spacer and 5.8S DNA from isolates of Gaeumannomyces graminis, Phialophora graminicola and other root-infecting fungi, isolated mostly from cereals and grasses. Different restriction enzymes were used to digest these amplified rDNAs to find polymorphisms useful in identification. Most of the enzymes tested were useful for discriminating between G. graminis and P. graminicola, and three enzymes (Dde I, Hae III and Hha I) could be used to distinguish between the varieties of G. graminis (tritici, avenae and graminis). However, a few atypical isolates gave intermediate RFLP patterns. The method was found to discriminate between Gaeumannomyces-Phialophora fungi and other organisms and identify G. graminis var. tritici and P. graminicola on infected wheat roots. The approach is a useful addition to the techniques available for the identification of fungi in the Gaeumannomyces-Phialophora complex.