Hevea brasiliensis (Willd. ex A.Juss.) Müll.Arg., the world’s primary source of natural rubber, faces increasing threats from emerging diseases in tropical cultivation regions. During recent field surveys in Yunnan and Hainan provinces of China, previously uncharacterized brown, water-soaked necrotic lesions were observed on tender stems and leaves of rubber trees. This study aimed to identify the causal pathogen, characterize its biological traits, and evaluate candidate fungicides for disease management. The pathogen was isolated via tissue explant methods and identified through morphological observation combined with multigene phylogenetic analyses based on the internal transcribed spacer (ITS) region, large subunit (LSU) ribosomal DNA, and cytochrome c oxidase subunits I and II (coxI and coxII) sequences. Pathogenicity was rigorously confirmed by fulfilling Koch’s postulates on rubber tree seedlings. The isolates produced spherical to ovoid, papillate sporangia, and phylogenetic reconstruction strongly supported clustering them with Phytopythium vexans. The pathogen grew optimally at 16–31 °C, with growth ceasing at 35 °C. Fungicide sensitivity assays revealed that metalaxyl exhibited the strongest inhibitory activity against mycelial growth, with half-maximal effective concentration (EC₅₀) values as low as 0.04 μg/mL. To our knowledge, this is the first report of P. vexans causing foliar and stem necrosis on H. brasiliensis. These findings provide a theoretical foundation for accurate disease diagnosis, epidemiological surveillance, and the development of effective chemical control strategies for rubber plantations.