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Cork oak forests are of immense importance in terms of economic, cultural, and ecological value in the Mediterranean regions. Since the beginning of the 20th century, these forests ecosystems have been threatened by several factors, including human intervention, climate change, wildfires, pathogens, and pests. Several studies have demonstrated the primary role of the oomycete Phytophthora cinnamomi Ronds in the widespread decline of cork oaks in Portugal, Spain, southern France, and Italy, although other congeneric species have also been occasionally associated. Between 2015 and 2019, independent surveys were undertaken to determine the diversity of Phytophthora species in declining cork oak stands in Sardinia (Italy). Rhizosphere soil samples were collected from 39 declining cork oak stands and baited in the laboratory with oak leaflets. In addition, the occurrence of Phytophthora was assayed using an in-situ baiting technique in rivers and streams located throughout ten of the surveyed oak stands. Isolates were identified by means of both morphological characters and sequence analysis of internal transcribed spacer (ITS) regions of ribosomal DNA. In total, 14 different Phytophthora species were detected. Phytophthora cinnamomi was the most frequently isolated species from rhizosphere soil, followed by P. quercina, P. pseudocryptogea, and P. tyrrhenica. In contrast, P. gonapodyides turned out to be the most dominant species in stream water, followed by P. bilorbang, P. pseudocryptogea, P. lacustris, and P. plurivora. Pathogenicity of the most common Phytophthora species detected was tested using both soil infestation and log inoculation methods. This study showed the high diversity of Phytophthora species inhabiting soil and watercourses, including several previously unrecorded species potentially involved in the decline of cork oak forests.