Plant diseases, particularly root rot caused by Phytophthora species, pose a significant threat to plants. In this study, we investigated the antagonistic activity of a Bacillus velezensis strain (Bv-SM1) against Phytophthora palmivora isolates, NKST002 and CP002, which cause root rot in durian. In vitro assays using dual-plate, pour-plate, and volatile organic compounds demonstrated a strong inhibition of Phytophthora mycelial growth by Bv-SM1. Phylogenomic analysis based on 1000 genes confirmed that Bv-SM1 is most closely related to B. velezensis. Genome analysis revealed the presence of key genes that contribute to biocontrol activity, including genes encoding cell wall-degrading enzymes (β-glucanase and cellulase) and siderophore production. Additionally, 13 biosynthetic gene clusters are responsible for the production of various antimicrobial compounds, such as fengycin, bacillaene, macrolactin, and bacilysin. These findings are the first to demonstrate the potential of Bv-SM1 as a promising biocontrol agent for managing Phytophthora-induced root rot in durian, with potential applications in other crops.