Sequence analysis of the internal transcribed spacer (ITS) regions I and II of ribosomal DNA were used to deduce evolutionary relationships among 15 Phytophthora species. Analysis of papillate, semi-papillate and non-papillate species showed that sporangium papillation has phylogenetic significance, with the three morphological groups each forming separate clusters. Within the P. megasperma species complex, separate evolutionary lines were identified for P. medicaginis, P. trifolii, and P. sojae formerly regarded as formae speciales of P. megasperma, confirming their recent reclassification as biological species. rDNA sequence analysis was able to distinguish P. cryptogea and P. drechsleri isolates indicating a valid basis for speciation. P. macrochlamydospora from soybean, which has only been observed in Australia, was closely related to P. sojae, indicating possible common ancestory.