Cilia and flagella change motility in response to stimuli, which induce activation of axonemal dyneins through signal transduction across plasma membrane. The activation mechanism is still not fully understood, but the regulatory subunits of axonemal dyneins play critical roles. In this chapter, the molecular compositions of axonemal dynein and the regulatory complexes are described and compared using Chlamydomonas and Ciona sperm as specific examples.