Two non-papillate species of Phytophthora are the principal cause of pistachio gummosis in Iran. Their previous description as P. megasperma and P. drechsleri was re-examined in the light of RFLPs and sequence comparisons of internal transcribed spacer (ITS) regions of rDNA. Both taxa were more closely related to a clade comprising P. sojae, P. cajani, P. vignae, P. melonis and P. sinensis than to the unrelated P. megasperma s. str. or P. drechsleri. The P. megasperma-like isolates from pistachio differed from all the above taxa in morphology, ITS sequence and AFLP patterns, and are described as a new species, P. pistaciae. The P. drechsleri-like isolates from pistachio had identical ITS sequences to those of P. melonis, P. sinensis and P. drechsleri-like isolates from cucurbits in Iran and the AFLP profiles of P. melonis, P. sinensis and the P. drechsleri-like isolates from pistachio were virtually identical. This and other published isozyme and mtDNA evidence suggests these taxa should be considered conspecific and all subsumed within P. melonis with a revised host range and geographical distribution. The relationships of P. melonis and P. pistaciae with other members belonging to the same ITS clade are considered.