The ZmEREB46 （Zm00001d015759） gene as a member of the ERF family in maize was cloned to identify and mine the resistance genes to waterlogging stress in maize.The resequencing，functional mutation site and expression pattern of the ZmEREB46 gene were analyzed.The role of the ZmEREB46 gene in waterlogging tolerance in Arabidopsis thaliana was preliminarily studied.The results showed that ZmEREB46 encoded one AP2/EREBP transcription factor.There was a G/A conversion and a 911 bp fragment insertion in the coding and promoter regions of the ZmEREB46 gene in the waterlogging susceptible inbred line A3239，compared to the waterlogging tolerant inbred line A3237.The insertion of a 911 bp fragment in the waterlogging susceptible inbred line A3239 significantly inhibited the expression of ZmEREB46.The results of subcellular localization showed that ZmEREB46 was localized in the nucleus.The results of quantitative PCR （qRT-PCR） analysis showed that ZmEREB46 was up-regulated by waterlogging stress，and the expression level of ZmEREB46 in A3237 was two-fold higher than that in A3239 after 8 h of waterlogging treatment.The overexpression of ZmEREB46 in A. thaliana improved the waterlogging tolerance of A. thaliana at the stage of seedling.