Abstract: We explored how Batrachium bungei (Steud.) L. Liou has adapted to extreme high-altitude environments. We used transcriptome sequencing and bioinformatics analysis of seven populations of B. bungei (ML, MZ, WQ, YH, YBJ, XB, ZR). Based on Pearson correlation analysis and principal component analysis (PCA), results showed that the gene expression of each population was highly similar. Differential gene enrichment analysis showed that phenylpropanoid biosynthesis was significantly enriched in five different groups. In addition, flavonoid biosynthesis, carotenoid biosynthesis, phenylalanine tyrosine and tryptophan biosynthesis, plant hormone signaling transduction, MAPK signaling pathway, and plant-pathogen interaction were significantly enriched. Compared with low-altitude populations, flavonoid biosynthesis genes (HHT1, HCT, F3'H, CHS, CYP73A, CCOAOMT5, CYP98A) were significantly up-regulated in the high-altitude populations, and their expression levels were significantly higher than those in the low-altitude (MZ) population. These results indicate that B. bungei adapted to the high-altitude environment of the Qinghai-Tibet Plateau mainly through multi-pathway participation and the regulation and expression of key genes.