There are approximately 60 described species in the genus Phytophthora. Despite the economic and ecological damage they cause worldwide, the genus is poorly understood. A major difficulty, with implications for scientific communication as well as phytosanitary regulations, is species identification. With a paucity of stable morphological characters, even specialists can have difficulty in identification beyond the genus level. Appropriate molecular methods offer an objective alternative. In this paper, the utility of the internal transcribed spacer (ITS) regions of the subunit which encodes ribosomal RNA is discussed. At the Scottish Crop Research Institute, an examination of the ITS restriction digest patterns of over 450 Phytophthora isolates representing almost all known taxa has allowed an evaluation of the method. Sophisticated band-matching software has been used to compare new isolates rapidly with those in the database. The limitations of such methods are also discussed. In some cases (e.g. closely related taxa with identical ITS regions, or where discrimination at the intraspecific level is needed), amplified fragment length polymorphism (AFLP) analysis is necessary. The database of AFLP fingerprints developed in Plant Research International is discussed in this context.