The most conspicuous brain microtubule-associated protein, MAP-2, has been shown to contain 8-10 mol of covalently bound phosphate/mol, as isolated. The MAP-2-associated cAMP-dependent protein kinase can add 10-12 more phosphates, using cycled microtubule preparations, but it does not catalyze exchange between ATP and the pre-existing protein phosphate. We now show that the phosphates that turn over in vivo, after intracerebral injection of 32Pi, are primarily in the projection domain of MAP-2, whereas the sites phosphorylated in vitro are more concentrated in the binding domain. Phosphoserine and phosphothreonine were recovered in a 6:1 ratio from partial acid hydrolysates of MAP-2 phosphorylated either in vivo or in vitro. A protein phosphatase, purified from brain, released residues from in vitro sites in both domains. The enzyme did not release appreciable phosphate that had turned over in vivo, and similar specificity was shown by three other purified protein phosphatases: calcineurin (also from brain) and smooth muscle phosphatases I and II. Thus, even in the projection domain, different sites may be involved.