Abstract High-throughput sequencing (HTS) has instigated a paradigm shift in plant pathology, showcasing its transformative role in the management of plant diseases. As a powerful tool, HTS aids in identifying pathogens and enhances disease management strategies by detecting novel and emerging pathogens, tracking disease outbreaks, and contributing to developing disease-resistant cultivars. Despite these benefits, the implementation of HTS faces obstacles due to the complexity of data interpretation and economic factors that affect its widespread adoption. This comprehensive review summarizes the strengths, limitations, and opportunities associated with using HTS in managing plant diseases. The article also delves into the prospects of HTS, incorporating technological advancements, synergy with complementary methodologies, capacity-building initiatives, and the development of best practices and guidelines. By acknowledging and addressing these obstacles while harnessing the full capabilities of HTS, we advocate for a refined approach to managing plant diseases. This approach is critical for ensuring global food security, especially in the context of a growing global population and climate change.
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