The B variant of beta-casein was phosphorylated with [gamma-32P]ATP using four different protein kinases isolated from rabbit reticulocytes. Casein was maximally phosphorylated by the individual protein kinase activities and subjected to chymotrptic digestion. The peptides were separated by a two-dimensional peptide fingerprinting technique, and the phosphorylated peptides were identified by autoradiography, The two phosphorylated peptides obtained from the action of casein kinase I were shown to have different migration patterns from those obtained with casein kinase II. The cAMP-regulated protein kinases had the same substrate specificity with beta-casein B, and the two phosphorylated peptides obtained using these enzymes were distinct from those phosphorylated by the cAMP-independent enzymes. Thus, the different protein kinases can be identified by substrate specificity using beta-casein.