Plasmids are mobile DNAs that can adjust host cell functions for their own amplification and dissemination. We identified Quorum sensing flagella small RNA regulator (QfsR), a small RNA, transcribed from the virulence tumour-inducing (Ti) plasmid in the phytopathogen Agrobacterium fabrum. QfsR is widely conserved throughout RepABC plasmids carried by Rhizobiaceae. Target prediction, expression analysis and site-direct mutagenesis experiments showed that QfsR directly pairs within polycistronic mRNAs transcribed from chromosome (genes involved in flagella apparatus) and Ti plasmid (genes involved in conjugative transfer). QfsR leads to a coordinated expression of whole polycistronic mRNA molecules. Whereas a lack of QfsR represses motility, its overproduction increases the quorum sensing signal accumulation and the Ti plasmid conjugative transfer. Based on these observations, we propose QfsR as a hub connecting regulatory networks of motility and plasmid conjugative transfer. To our knowledge, QfsR is the first example of a plasmid-encoded sRNA that controls chromosomal polycistronic gene expression.