Soilborne diseases caused by pathogens such as Phytophthora, Rhizoctonia, Fusarium, Verticillium, and Pythium species are the most important diseases of woody ornamentals. Ginkgo (Ginkgo biloba) and red maple (Acer rubrum) ‘October Glory’ plants grown in containers and fields in Tennessee have shown root and crown rot symptoms with dark brown to black lesions in 2017 and 2018. The objective of this research was to isolate and identify pathogens affecting ginkgo and red maple plants in nurseries of Tennessee and develop fungicide/biofungicide management recommendations for nursery producers. Isolations were made from the infected roots. Several Phytophthora-like colonies with spherical zoospores, filamentous to globose oogoni, and whitish mycelium, were isolated on V8-PARPH medium. For confirming identity, total genomic DNA was extracted followed by the sequence analysis of the internal transcribed spacer (ITS) regions, and large subunit (LSU) of the nuclear ribosomal RNA (rRNA) as well as cytochrome c oxidase subunit I (Cox I) and cytochrome c oxidase subunit II (Cox II) of mitochondrial DNA (mtDNA). Based on morphological and molecular analysis, Phytopythium vexans was described as a causal agent of crown and root rot from the infected ginkgo and red maple plants. To complete Koch’s postulates, a pathogenicity test was performed by drenching 100 ml V8 agar medium slurry of P. vexans inoculum on 1-year-old potted ginkgo plant root systems as well as red maple ‘October Glory’. Necrotic lesion development was observed in the root system 45 days after inoculation and P. vexans was re-isolated from the roots of both ginkgo and red maple. All control ginkgo and red maple plants remained disease-free and no pathogen was re-isolated. In addition, the efficacy of fungicides, biofungicides, fertilizer and host-plant defense inducers (traditionally recommended for management of oomycete diseases) for control of Phytopythium crown and root rot was evaluated on ginkgo and red maple ‘October Glory’ seedlings in greenhouse and field trials. The fungicides such as Empress Intrinsic, Pageant Intrinsic, Segovis and Subdue MAXX were effective in both greenhouse and field trials, and the biofungicide Stargus reduced the disease severity caused by pathogen P. vexans on ginkgo and red maple plants in greenhouse trials. These results will help nursery producers to make proper management decisions for newly reported Phytopythium crown and root rot disease of ginkgo and red maple plants.