Phytophthora quercina, a new species associated with oak decline in Europe, has been assigned to Waterhouse's Group I of Phytophthora. The level of intraspecific variation and evidence of affinities to other Group I species and another, as yet unidentified, species from oak, were examined at the molecular level using four random ten-mer primers to amplify total DNA (RAPDs). Sequences and restriction fragment length polymorphisms of a 900 bp PCR product consisting of the ITS1 and ITS2 regions, and the 5.8S subunit of ribosomal DNA were also examined to estimate relatedness to a broader range of Phytophthora species. The RAPD banding patterns of ten isolates of P. quercina from eight sites in Germany, Hungary and Italy were almost identical and distinct from all the other species tested. Their ITS restriction fragment patterns were also identical, as were the ITS sequences of four selected isolates. Phylogenetic analysis of the ITS sequence data confirmed its unique position in this section of the genus which comprises P. quercina, another five Group I species, P. infestans (Group IV) and P. nicotianae (Group II). Isolates of P. quercina formed a distinct branch at the base of this clade showing no close affinities with any other species. Such data support morphological, physiological and pathological evidence that P. quercina is distinct, although it has some affinity with the other Group I species. The results support earlier reports that Waterhouse's groupings of morphospecies do not fully correspond to phylogenetic relationships indicated by molecular studies. The unidentified Phytophthora sp. 2 from oak was closely related to P. ilicis (Group IV); both were distinct on molecular criteria from all other species in the study.