Citrus plants are sensitive to waterlogging, and the roots are the first plant organ affected by hypoxic stress. TheAP2/ERF(APETALA2/ethylene-responsive element binding factors) can modulate plant growth and development. However, the information onAP2/ERFgenes in citrus rootstock and their involvement in waterlogging conditions is limited. Previously, a rootstock cultivar,Citrus junoscv. Pujiang Xiangcheng was found to be highly tolerant to waterlogging stress. In this study, a total of 119AP2/ERFmembers were identified in theC. junosgenome. Conserved motif and gene structure analyses indicated the evolutionary conservation ofPjAP2/ERFs. Syntenic gene analysis revealed 22 collinearity pairs among the 119PjAP2/ERFs. The expression profiles under waterlogging stress showed differential expression ofPjAP2/ERFs, of which,PjERF13was highly expressed in both root and leaf. Furthermore, the heterologous expression ofPjERF13significantly enhanced the tolerance of transgenic tobacco to waterlogging stress. The overexpression ofPjERF13decreased the oxidative damage in the transgenic plants by reducing the H2O2and MDA contents and increasing the antioxidant enzyme activities in the root and leaf. Overall, the current study provided basic information on the AP2/ERF family in the citrus rootstock and uncovered their potential function in positively regulating the waterlogging stress response.