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Horizontal gene transfer facilitates dissemination of favourable traits among bacteria. However, foreign DNA can also reduce host fitness: incoming sequences with a higher AT content than the host genome can misdirect transcription. Xenogeneic silencing proteins counteract this by modulating RNA polymerase binding. In this work, we compare xenogeneic silencing strategies of two distantly related model organisms:  Escherichia coli  and  Bacillus subtilis . In  E. coli , silencing is mediated by the H-NS protein that binds extensively across horizontally acquired genes. This prevents spurious non-coding transcription, mostly intragenic in origin. By contrast, binding of the  B. subtilis  Rok protein is more targeted and mostly silences expression of functional mRNAs. The difference reflects contrasting transcriptional promiscuity in  E. coli  and  B. subtilis , largely attributable to housekeeping RNA polymerase σ factors. Thus, whilst RNA polymerase specificity is key to the xenogeneic silencing strategy of  B. subtilis , transcriptional promiscuity must be overcome to silence horizontally acquired DNA in  E. coli .

Xenogeneic silencing strategies in bacteria are dictated by RNA polymerase promiscuity