In recent years, the role of bacterial sRNAs in adversity tolerance and pathogens has attracted increasing attention. A great number of virulence-related sRNAs were reported in a variety of human pathogens. However, only a few sRNAs from aquatic pathogens were reported. In our previous study, a novel sRNA, sR158, was identified in Edwardsiella piscicida, an important aquatic pathogen, but its function remains unknown. In the same aquatic pathogen, we also identified a type II TA system, YefM-YoeB, in another study. In the current report, we found that the expression of yefM-yoeB in E. piscicida was regulated by sR158, which is dependent on the RNA chaperon Hfq. The deletion of sR158 reduced bacterial tolerance to oxidation pressure, enhanced bacterial capacity for biofilm formation, increased bacterial adhesion and invasion of host cells and immune tissues, and boosted bacterial general virulence, which are consistent with the effects caused by the deletion of YefM-YoeB. These findings indicate that sR158 participates in the stress resistance and virulence of E. piscicida by regulating YefM-YoeB. Our result is the first report that the type II TA system is regulated by sRNA, which provides new insights into the regulatory role of bacterial sRNA.