Abstract Calcineurine B-like proteins (CBLs) and their interacting protein kinases (CIPKs) in Arabidopsis relay the Ca2+ signals elicited by a variety of stresses. Because distinct CBL–CIPK complexes, respectively, play a role in a different signaling pathway, understanding of the entire network of the CBL–CIPK association is essential to unravel the Ca2+-mediated stress responses. In this study, we have identified 9 CIPKs that interact with the CBL3 Ca2+ sensor using the yeast two-hybrid system. They all contained a highly conserved region, spanning 32 amino acids in length, in the nonkinase domain. Further analyses with CIPK11, one of the CBL3-interacting CIPKs, revealed that the C-terminal region containing the conserved domain was required and sufficient for interaction with CBL3. In vitro interaction assays demonstrated that the CBL3–CIPK11 complex formed in a Ca2+-dependent manner. Expression of the CIPK11 gene was detected in the roots, the shoot apex, the axils of cauline leaves, and the anthers of the flowers. Taken together, our findings suggest that CIPK11 may associate with CBL3 in vivo, thereby mediating the Ca2+ signals downstream.