The causal agent of stem and root rot of cowpea, Phytophthora vignae, is a widely distributed species of the Phytophthora genus. Here, we generate a high-quality complete genome assembly of P. vignae PSY2020 (89.39 Mb, N₅₀ 2.99 Mb) from China, using Oxford Nanopore Technologies (ONT) sequencing. The genome assembly completeness as evaluated by benchmarking universal single-copy orthologs was 94.51% at the eukaryote level. We identified 42.54% as repeat sequences and a total of 20,536 protein-encoding genes, of which 15,184 genes could be annotated. And we also identified 924 candidate RXLR effectors in the genome assembly. The described genome sequence will provide a valuable resource for better understanding of pathogenicity mechanisms of P. vignae and help in uncovering phylogenetical classification of Phytophthora species. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2021.