Investigation of the endoplasmic reticulum-associated degradation (ERAD) system in plants led to the identification of ERAD-Mediating RING finger protein (EMR) as a plant-specific ERAD E3 ligase from Arabidopsis. EMR was significantly upregulated under ER stress conditions. The EMR protein purified from bacteria displayed high E3 ligase activity, and tobacco leaf-produced EMR mediated mildew resistance locus O-12 (MLO12) degradation in a proteasome-dependent manner. Subcellular localization and co-immunoprecipitation analyses showed that EMR forms a complex with ubiquitin-conjugating enzyme 32 (UBC32) as a cytosolic protein. Mutation of EMR and RNA interference (RNAi) increased the tolerance of plants to ER stress. EMR RNAi plants in a bri1-5 background partially recovered the brassinosteroid-insensitive phenotypes of the original mutant plants and increased ER stress tolerance. The present results suggest that EMR is a novel plant-specific E3 ligase that mediates the removal of misfolded proteins under ER stress.