Elsinoë annonae is a fungal pathogen that causes the fruit scab disease in edible-tea oil plant (Camellia oleifera Abel). The absence of assemble genome resources for this fungus hampers functional genetic studies into pathogenesis mechanism of E. annonae. This study reports the genome assembly of an E. annonae strain SM-YC-2 collected from tea oil tree fruits with scab disease in Fujian Province, China. Combining 16.44 Gb PacBio Sequel II long reads and 5.13 Gb Illumina NovaSeq reads, we generated 25.93-Mb (99.19% of expected genome size) high-quality genome assembly with 52.66% GC content, 5.05% repeats, and over 98% BUSCO completeness for E. annonae strain SM-YC-2 . It consists of 14 contigs with N50 of 2.83 Mb (L50: 4). The genome assembly contains 9,581 protein-coding genes coded 10,035 proteins, including 2,111 pathogen-host interaction genes (PHI), 399 carbohydrate-active enzymes (CAZys), 237 membrane transport proteins, 499 candidate secreted proteins (including 76 cytoplasmic effectors and 165 apoplastic effectors), and 24 secondary metabolite biosynthetic gene clusters (SMBGCs). These high-quality genome assembly resources will facilitate functional genomic characterization studies to enhanced insights into the pathogenicity mechanism of E. annonae and support the development of molecular-based control strategies.