Riboswitches are RNA elements that sense metabolites and control gene expression. Recently, the yybP-ykoY riboswitches were found to sense manganese (Mn2+) and regulate the expression of diverse genes. Here, we show that the leader RNA (a yybP-ykoY RNA) of yebN in Xanthomonas oryzae pv. oryzae also functions as a sensor of Mn2+. This leader RNA detects Mn2+ levels in plants and is essential to X. oryzae pv. oryzae virulence. Our data also indicate that Mn2+ is not only required as a microelement for plant growth but also acts as a defense molecule to inhibit pathogen growth. This finding highlights that Mn2+ plays important roles in pathogen-plant interactions and that the yebN leader RNA can be a target candidate for anti-X. oryzae pv. oryzae drug development.