Serotonin, an activator of adenylate cyclase, stimulates motility in molluscan gill cilia and sperm flagella. To determine and compare potential targets of cAMP action, dynein was prepared from the lateral gill.cilia and sperm flagella of the mussel Mytilus edulis and the clam Spisula solidissima. In the flagella of both species, high-salt extraction removes about half of the ATPase activity, half of the alpha and beta heavy chains, and the outer arms. The dynein from both species sediments at 18-20 S, contains two or three intermediate chains, and three light chains. High-salt plus detergent removes most of the remaining dynein ATPase, alpha and beta heavy chains, and inner arms, also yielding a stable 18-20 S particle. In gill cilia of both species, high-salt extraction removes only 12-18% of the ATPase, up to 1/3 of the alpha heavy chains, an equivalent amount of beta heavy chain, and a subset of the outer arms. The dynein sediments at 18-20 S and, in Spisula, the heavy, intermediate, and light chains precisely co-sediment. High-salt plus detergent removes another 1/3 of the alpha heavy chains, an equivalent amount of beta heavy chain, and the remaining outer arms. The ATPase sediments mainly as a 13-14 S form showing considerable dissociation of co-sedimenting intermediate and light chains. The inner arms and at least half of the ciliary dynein ATPase activity remain unextractable, corresponding in mass mainly to an apparent beta heavy chain that is vanadate-cleavable. Cyclic AMP-dependent, calcium-independent phosphorylation takes place on specific dynein light chains in cilia but on only the dynein alpha heavy chain in flagella. Pre-activation of the flagella prevents subsequent addition of labeled phosphate. Phosphorylation has no effect on the steady-state ATPase properties. The single phosphate added to the flagellar alpha chain is located within the LUV1 vanadate photocleavage fragment. Considering the probable locus of the light chains and the site of the alpha heavy chain phosphorylation, both beyond the active site and toward the base of the molecule, these distinct phosphorylations may regulate dynein action by modulating arm flexibility or interaction.