Glycogen synthase was isolated from extracts of mouse diaphragm muscle by immunoprecipitation with specific antibodies raised against the rabbit muscle enzyme. A procedure was developed which permitted phosphorylation of the immunoprecipitated enzyme by several purified protein kinases. Peptide mapping techniques (including reverse-phase HPLC and thin-layer electrophoresis and chromatography) were used to compare tryptic phosphopeptides of the rabbit and mouse muscle enzymes. The results demonstrated a high degree of similarity in the chemical properties of these peptides, suggesting significant homology around the phosphorylation sites in these proteins. Thus, mouse peptides corresponding to the rabbit muscle peptides containing sites 1a, 1b, 2, 3, and 5 were identified, with protein kinase recognition specificities identical to those of the rabbit enzyme. The study indicates significant conservation in the muscle isozymes of glycogen synthase between mouse and rabbit as well as a similar distribution of phosphorylation sites throughout the enzyme subunit.