FOXI1 plays an important role in driving cell lineage determination of ionocytes at bronchial epithelial lining. However, its binding sites and target genes remained unclear. Here in this study, RNA-seq and CUT&Tag-seq technology were performed on FOXI1-expressing bronchial epithelial cells. RNA-seq results showed 1,773 genes were significantly upregulated more than a log-fold-change of two. 65 genes were annotated as a bronchial epithelial marker gene and 35 were categorized as ionocytes, including CFTR and ASCL3. Furthermore, CUT&Tag-seq captured 103,341 unique peaks in the genome region. Most of these binding peaks are located at promoter or intergenic regions and 20,605 genes were identified as FOXI1 binding genes. Interestingly, no peaks were directly annotated to ASCL3 but C11orf16, which locates downstream of ASCL3 within 5kb. This suggests FOXI1 may function with other co-activators or interact at trans-regulatory regions to regulate gene expression. In conclusion, our data identified the genome-wide binding sites of FOXI1.