The tea‐oil tree Camellia oleifera is native to China and is cultivated in many parts of southern China. Anthracnose on Ca. oleifera is one of the most serious diseases in China. The major causal pathogen of tea‐oil anthracnose is Colletotrichum fructicola, but the detailed molecular mechanisms of its pathogenicity are still largely unclear. Vacuolar protein sorting 39 (Vps39) is a component of the homotypic fusion and vacuole protein sorting (HOPS) complex. To investigate the role of HOPS proteins in the fungal plant anthracnose pathogen C. fructicola, the CfVPS39 gene was deleted. This resulted in reduced mycelial growth, conidial production and complete loss of pathogenicity on tea‐oil leaves and fruits. In addition, ∆Cfvps39 showed increased sensitivity to cell wall stress, osmotic stress and endoplasmic reticulum stress. Further analysis revealed that CfVps39 is required for appressorium formation and homotypic vacuole fusion, both important for fungal pathogen invasion. Our study provides evidence that CfVps39 has a role in conidiation, stress response, appressorium formation, homotypic vacuole fusion and virulence against tea‐oil. This research not only provides the theories for revealing the pathogenic molecular mechanism of C. fructicola, but also has important guiding significance to reveal new fungicide targets to control this devastating disease.