Microtubule-associated proteins (MAPs), isolated from brain tubulin, bound to and saturated outer fibers of Chlamydomonas flagella. MAPs present on these microtubules prevented the subsequent recombination of dynein. MAPs also bound to intact axonemes and thus did not specifically bind to the dynein binding sites on the A subfiber. A molar ratio of 1 mole MAP2 per 27 moles tubulin dimers at saturation of the outer fibers with MAP2 suggested that MAPs could effectively interfere with dynein recombination only if the MAPs were near the dynein binding sites to sterically prevent binding. However, electron microscopic observations indicated that MAPs were not localized but, instead, were dispersed around the outer fibers. In addition, MAP2 present at saturating amounts on in vitro assembled brain microtubules had no significant effect on dynein binding. Dynein-decorated microtubules contained clusters of arms suggesting that there may be cooperative interaction between the arms during dynein binding. Because the A subfiber of axonemes contains sites to which dynein preferentially attaches, MAPs may prevent recombination by interfering with cooperative binding to these specific sites. Dynein presumably binds with equal affinity to any protofilament on in vitro assembled microtubules, and, therefore, the MAPs may not be capable of effectively interfering with cooperative binding of dynein to these microtubules.