We analyzed the morphology and phylogenetic placement of six isolates of Phytopythium belonging to P. helicoides, P. palingenes and P. vexans that were isolated from water bodies and substrates used for hydroponically grown crops. The molecular data are from the partial large subunit and the complete internal transcribed regions of the ribosomal DNA. These three species are characterized by the presence of ovoid to globose zoosporangia with papillae, internal proliferation as in Phytophthora and mode of zoospore discharge as in Pythium. All isolates showed high morphological and phylogenetic similarity with members of the Clades II and III of Phytopythium. In this paper, Phytopythium palingenes is included for the first time in phylogenetic analyses and our ITS and LSU phylogenies indicated that Aquaperonospora taiwanensis is a synonym of Phytopythium helicoides.