To investigate the mechanism by which Drosophila generates multiple calcium/calmodulin-dependent protein kinase II (CaM kinase) subunits, CaM kinase cDNAs were isolated and sequenced. Eight different cDNA sequences, varying only at the junction of the regulatory and association domains of the kinase, were obtained. These results indicate that the diversity of CaM kinase in Drosophila is greater than previously appreciated and is generated by alternative splicing of a single gene. In situ hybridization showed CaM kinase mRNA is present in both neuronal and nonneuronal tissues in adult Drosophila. No differential tissue distribution of isoforms was observed.