【Objective】Soil alkalinity is a widespread environmental problem that limits crop yield. Up to 831 million hectares of land are under salt stress on the earth, and about half are being alkalinized. Under alkali stress, plants are exposed to both salt and high pH. Moreover, high pH stress is a more significant factor in limiting plant growth than salt stress. High pH stress inhibits plant growth by imposing adverse effect on roots, such as increasing ion imbalance, disrupting cellular pH stability and decreasing nutrient solubility. However, it remains unknown how transcription responds to high pH stress for regulation and its mechanism. Therefore, this paper tries to elucidate molecular mechanism of high pH tolerances of Arabidopsis with the aid of high throughput biotechnology. The research is essential to breeding high and stable yield crops. 【Method】 In recent years, high throughput sequencing has been rapidly developed and used in genome-wide gene expression profiling of Arabidopsis, rice and soybean. In this paper, a stable pH experiment system was established and transcriptional profiling of the root of Arabidopsis cultivated in high pH medium for 7 days was conucted using RNA-seq. Then differently expressed genes (DEGs) in response to high pH stress were presented and annotated. In the end, important high pH responsive genes and their putative upstream transcription factors were identified.【Result】The following findings were obtained. It was found that under high pH stress, growth of the primary root of Arabidopsis was significantly limited. Transcriptome sequencing of Arabidopsis root under normal pH (6.0) and high pH (8.0) were performed. Of the 1129 DEGs analyzed, 329 were identified as up-regulated genes and 800 as down-regulated genes. GO (Gene Ontology) functional categorization shows that these DEGs are highly related to abiotic stimulus, transcription, cell organizations and biogenesis, ion transport, protein metabolism and signal transduction. In addition, several genes were determined to be responsive to high pH identified. For example, water channel gene PIP2;4 and PIP2;5 , Al-activated malate transporter gene ALMT1 , K+ transporter gene HAK5 and calcium exchanger gene CAX7 were down-regulated after high pH treatment. Several encoding calcium binding proteins and calmodulin protein genes, such as MSS3, CBL7, CML23, CML37, CML38, were also down-regulated under high pH stress. Auxin responsive genes SAUR16, SAUR40, IAA4 and transport genes PIN5, PIN-LIKES7 and cytokinin biosynthesis genes LOG2 , LOG5, LOG6, LOG9 were expressed differently under high pH stress, suggesting that auxin and cytokinin play important roles in response to high pH. Meanwhile, identification of 97 differently expressed transcription factors (DE TFs) under high pH condition was performed. These DE TFs were included in 20 TF families, such as AP2/EREBP, MYB, WRKY, NAC, bHLH. Then a transcriptional regulatory network between DE TFs and important high pH responsive genes was constructed. It was found that DE TFs belonged to AP2/EREBP, WRKY, NAC and MYB TF families, such as DREB2A, WRKY45 , NAC045 and MYB107 acted as the hub genes in this high pH responsive network.【Conclusion】In this paper, a comprehensive overview was presented of the transcriptomes of Arabidopsis root under high pH stress. Among them a total of 1129 genes were identified as high pH responsive DEGs, and frequently involved in transcription regulation, ion transport, cell wall organizations, Ca²⁺ signaling and hormones pathway. Furthermore, regulatory relationship between the DE TFs and high pH responsive genes were predicted. DE TFs belongimg to AP2/EREBP, WRKY, NAC and MYB families played core roles in this regulatory network, suggesting that these TFs play important roles in high pH stress response in Arabidopsis. Overall, all the findings in this study may serve as a important theoretical basis for breeding of alkaline-tolerant crops.