Clostridium autoethanogenum is a gram-positive bacterium capable of growth on CO and/or CO₂+H₂ (syngas) as sole carbon source¹. The bacterium ferments syngas into acetyl-CoA using the Wood-Ljungdahl pathway². C. autoethanogenum can also grow on fructose using the Embden–Meyerhof–Parnas glycolytic pathway³. Such contrasting metabolisms are ideal to compare transcriptional control of both metabolisms and here we used differential RNA sequencing (dRNA-seq) to generate the first map of transcriptional start sites (TSS) for a gas-fermenting organism. This map revealed a number of misannotations and 140 genes were re-annotated. As in other organisms, most TSSs were found within a 20-50 nucleotide region upstream of annotated genes. The main promoter motif was associated with the sigma factor σ⁷⁰ family, whereas most of the TSSs for the Wood-Ljungdahl pathway genes were found to be under the regulation of a new promoter motif, described here for the first time. Internal, antisense and orphan TSSs mapping reveal a high level of transcriptional complexity and suggest that the regulation that was thought to be relatively simple, is far more complex and far from being fully understood.