AP2/ERF(APETALA2/ethylene-responsive factor) superfamily is one of the largest gene families in plants and has been reported to participate in various biological processes, such as the regulation of biosynthesis of active lignan. However, few studies have investigated the genome-wide role of the AP2/ERFsuperfamily in Isatis indigotica. This study establishes a complete picture of the AP2/ERFsuperfamily in I. indigoticaand contributes valuable information for further functional characterization of IiAP2/ERFgenes and supports further metabolic engineering.