Calmodulin (CaM), a key Ca2+ sensor in eukaryotes, regulates diverse cellular processes by interacting with many proteins. To identify Ca2+/CaM-mediated signaling components, we screened an Arabidopsis expression library with horseradish peroxidase-conjugated Arabidopsis calmodulin2 (AtCaM2) and isolated a homolog of the UBP6 deubiquitinating enzyme family (AtUBP6) containing a Ca2+-dependent CaM-binding domain (CaMBD). The CaM-binding activity of the AtUBP6 CaMBD was confirmed by CaM mobility shift assay, phosphodiesterase competition assay and site-directed mutagenesis. Furthermore, expression of AtUBP6 restored canavanine resistance to the Delta ubp6 yeast mutant. This is the first demonstration that Ca2+ signaling via CaM is involved in ubiquitin-mediated protein degradation and/or stabilization in plants.