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Despite the popularity of wild edible mushrooms due to their delectable flavor and nutritional value, the mechanisms involved in regulating and altering their taste remain underexplored. In this study, we analyzed the metabolome and transcriptome of <i>Boletus brunneissimus (B. brunneissimus) and Leccinum extremiorientale (L. extremiorientale)</i>, two <i>Boletus</i> species collected from different environments. Using UHPLC-MS, we annotated 644 peaks and identified 47 differential metabolites via OPLS-DA analysis. Eight of these were related to flavor, including L-Aspartic acid, Glycine, D-Serine, L-Serine, L-Histidine, Tryptophan, L-Isoleucine, Isoleucine, and alpha-D-Glucose. These differential metabolites were mainly concentrated in amino acid metabolism pathways. Transcriptome analysis revealed differential genes between <i>B. brunneissimus</i> and <i>L. extremiorientale</i>, which were enriched in protein processing in the endoplasmic reticulum, as well as differential genes of the same <i>Boletus</i> species in different environments that were enriched in the ribosome pathway. The combination of metabolome and transcriptome analyses highlighted Glycine, L-Serine, and L-Aspartic acid as the key compounds responsible for the differences between the two <i>Boletus</i> species. Using the O2PLS model and Pearson’s coefficient, we identified key genes that modulate the differences in metabolites between the two species. These results have significant implications for the molecular breeding of flavor in edible mushrooms.