Brain type II Ca2+/calmodulin-dependent protein kinase is a holoenzyme composed of several copies each of three subunits, alpha (50 kd), beta (60 kd), and beta' (58 kd), in varying proportions. The deduced amino acid sequences of alpha (reported here) and beta are highly similar but not identical. The major difference between them is the deletion from alpha of two short segments (residues 316-339 and 354-392 in beta). cDNAs that appear to encode beta' are identical to beta except for the deletion of a segment encoding residues 378-392. Thus, the structural differences among alpha, beta, and beta' arise primarily from deletions (or insertions) in a variable region lying immediately carboxyl to the protein kinase and calmodulin-binding domains. The alpha and beta subunits are encoded by distinct genes expressed primarily, if not exclusively, in brain. Rather than being encoded by a third gene, beta' may arise by alternative splicing of the beta gene transcript.