Glycogen synthase kinase 3 (GSK3)-like kinase play crucial roles in cell signaling pathways in both animals and plants. Here we showed that the BRASSINOSTEROID INSENSITIVE 2 (BIN2)/GSK3β-like kinase is controlled at the protein stability level in Arabidopsis thaliana, via a mechanism that involves an ubiquitin E3 ligase. Immunoprecipitation of the HA-tagged BIN2 protein complex followed by mass spectrometry identified BRASSINOSTEROID F-BOX 1 (BRF1) and BRF2 as interacting proteins. Validation in vitro by yeast two-hybrid analyses further confirmed the interacting complexes. These results, together with amino acid sequence alignment, suggest that BRF1 and BRF2 play redundant or overlapping roles in regulating BIN2 stability. Our results fill the gap in our understanding of the brassinosteroid signaling pathways, and elucidate a novel step of regulation that could integrate other signals, such as abiotic stress.