Food allergies (FAs) are a crucial public health problem and a severe food safety issue, resulting in an urgent need for an accurate method to detect the hundreds of allergens that exist in blind food systems. Current methods for detecting allergens</p><p>typically utilize ELISA, PCR or LC-MS, which can only simultaneously detect up to a dozen allergens in food samples with known components. In this study, we present a hybridization probe cluster-targeted next-generation sequencing (HPC-NGS) platform</p><p>for identifying potential allergens in blind food systems. This method successfully captured target DNA fragments and identified 112 allergens in a complex food system.</p><p>Additionally, the HPC-NGS provided expected allergenic species matching rates of 94.24-100% in single food materials and 99.87-99.98% in processed food products.