Objective A method for the identification of plant-derived allergens in food by using DNA barcoding technology was established.Methods psbA-trnH, trnl, and rbcl molecular markers were used to identify 11 plant-derived allergen species, including hazelnut, Brazil nut, macadamia nut, walnut, pecan, almond, sweet almond, cashew, pistachio, peanut, and soybean. The psbA-trnH, trnl, and rbcl gene sequences of each species were downloaded from GenBank, and sequence alignment, genetic distance calculation, and phylogenetic tree construction were performed using MEGA 11 software.Results Among the three gene sequences, the psbA-trnH sequence exhibits the most significant genetic distance variation, with an average interspecies genetic distance of 0.527 3, which is greater than those of the trnl and rbcl sequences. The analysis results of the phylogenetic trees constructed by the neighbor joining (NJ) method show that the phylogenetic trees constructed based on the psbA-trnH and trnl sequences have a good branching structure, and different species can be accurately clustered. In contrast, the phylogenetic tree constructed based on the rbcl sequence can not distinguish walnut from pecan or almond from sweet almond. Therefore, the psbA-trnH sequence is the optimal barcode for the identification of the 11 species. Combining the psbA-trnH barcode detection with high-throughput sequencing technology for the detection of 15 practical samples allows for the simultaneous detection of multiple allergen components.Conclusion The psbA-trnH sequence, as a DNA barcode, can accurately identify components of common plant-derived allergens.