Eukaryotic flagella and motile cilia from most species and organelles share a common “9 + 2” structure in which nine microtubule doublets surround two central singlet microtubules (the “central pair”, CP) [2, 12]. Adjacent microtubule doublets are connected by inner and outer dynein arms (IDA and ODA), while all doublets are linked to the CP by protein complexes called radial spokes (RS). To understand mechanisms of motility and regulation of eukaryotic flagella and cilia at the molecular level, three-dimensional (3D) structures of dynein and other component molecules in flagella/cilia are essential. Following the discovery of the dynein ATPase and its identification as a force-generating apparatus in dynein arms [15, 57], in situ structural analyses of dynein arms have been intensively carried out by various electron microscopy techniques.