Abstract: 【Objective】 The potential allergen genes were determined and the expression profiles in different tissues were evaluated using transcriptome sequencing of mango leaves and fruits to provide a theoretical basis for breeding lower allergenic mango cultivars.【Method】 The total RNA was extracted from mango fruits and leaves. Transcriptome sequencing(150 bp reads) using HiSeq 4000 was performed after the cDNA libraries construction. Unigenes were obtained with Trinity assemble of clean reads. The unigenes related to potential allergen genes were annotated using NR and Pfam databases. The expression levels of allergen genes in different tissues were determined using real-time fluorescence quantitative PCR(qRT-PCR). The epitopes of the allergen highly expressed in fruits combined with IgE antibody were obtained by Cluspro analysis.【Result】 A total of 230242 transcripts and 99328 unigenes were obtained. The N50 lengths of transcripts and unigenes were 2278 and 1183 individually, indicating the high assembly quality. Identified 66 potential allergen genes using NR and Pfam databases, including pollen allergens, Bet v family and NADPH-dependent FMN reductase. Six allergens showed no expression, 60 showed expression. There were 24 allergens and 36 allergens highly expressed in fruits and leaves, respectively. The qRT-PCR test showed that the expression of nine allergen genes in mango leaves and fruits was largely consistent with the RNA-Seq transcriptome expression analysis. Except that the expression of chitinase gene c64821.graph_c0 in leaves was significantly higher than flowers and fruits(P<0.05, the same below), the others were significantly expressed in flowers than leaves and fruits. The allergen c61327. graph_c0 highly expressed in fruit was used as the template to obtain homologous protein domain(PDB:4 Z8 W) by searching in the RCSB PDB database, the amino acid sequences combined with IgE epitope was 74-SFRQEVKTEKHGEFKVHLPFSVSEHV-99. The amino acid sequences of binding epitopes of allergen protein from different species were highly conserved.【Conclusion】 Different mango allergen genes have tissue expression specificity. Most genes are highly expressed in flowers, suggesting that people with allergic reactions after eating mango should avoid touching mango flowers. C61327. graph_c0 has cross-allergenic reactions with homologous allergens of other species.