One of the most important and challenging clades in Phytophthora spp. phylogenetic trees is Clade six of these taxa. Except a few species such as Phytophthora megasperma, P. gonapodyides, P. rosacearum and P. taxon Asparagi most of the related species have only been reported from forests, riparian ecosystems and irrigation reservoirs. During sampling from trees with crown and root rot symptoms in pistachio orchards of Kerman and Yazd Provinces, Iran, isolates with various patterns from single-stranded structural polymorphism of the ribosomal DNA were observed. All isolates were high-temperature tolerate, produced non-papillate, ovoid, obovoid to ellipsoid, and non-caducous sporangia, with internal and external proliferation, in some isolates with pedicel and sporangiophore swelling. All examined isolates were heterothallic, mating type A1, smooth thick-walled globus oogonia with amphigynous antheridia, globus plerotic oospores and all isolates were produced intercalary thin-walled chlamydospores in both liquid and solid media. The rDNA internal transcribed spacers (ITS) region, β-tubulin and the mitochondrially encoded cytochrome oxidase subunit 1 genes were amplified, clarified, sequenced and edited for all isolates. Multiple gene genealogy phylogenetic analysis based on maximum likelihood approach showed that the studied isolates were clustered in one group, along with a sequences of P. taxon Walnut, attributed to the first report of this taxon, isolated from walnut trees in the United States of America, in a monophyletic branch. In order to confirm the pathogenicity of the isolates, six-month-old pistachio and walnut seedlings were inoculated with different isolates. The disease symptoms in infected rootstocks were observed for six months, one hundred percent of seedlings, showed crown and root rot, wilt and decline branches symptoms in comparison with the controls. The formal nomenclature of this taxon, as another important member of the Clade six of Phytophthora spp. phylogenetic trees, is under investigation.