Bacillus amyloliquefaciens is an important industrial microbe for the production of many industrial enzymes and primary metabolites. Although the complete genome sequence of B. amyloliquefaciens has been now published, transcript structures of B. amyloliquefaciens remain poorly defined. In this study, high-throughput RNA sequencing (RNA-seq) technology was applied to dissect the transcriptome of B. amyloliquefaciens strain XH7. In total, 3936 out of a total of 4204 B. amyloliquefaciens genes (93.6%) were transcribed under the selected growth condition. Transcriptional start sites (TSS) of 1064 annotated genes and 749 operons were identified. To screen for strong promoters, a beta-galactoside reporter was fused to eight candidate promoters from 288 genes with higher expression levels (RPKM values) than the control gene P43-bgaB. The results illustrated that the candidate promoter Pr2 (promoter for the sigW gene) displayed the strongest beta-galactosidase specific activity during the post-log phase, suggesting that it could be used effectively for heterologous gene expression. The presented data will contribute to the further study of the B. amyloliquefaciens transcriptome by identifying useful promoters for industrial uses.