Thin section electron micrographs of rapidly fixed Chlamydomonas cells were used to establish a relationship between flagellar bends and orientation of the central pair microtubule complex. Using conditions that preserve flagellar waveforms during both forward swimming (asymmetric bends) and backward swimming (symmetric bends), we found that central pair orientation differs in bent regions and straight regions. During forward swimming, a plane through the two central pair microtubules is parallel to the bend plane throughout principal bends, in both effective stroke and recovery stroke phases of the beat cycle. In these curved segments, the C1 microtubule always faces the outer edge of the curve. This parallel orientation twists in straight regions both proximal and distal to bends. During backward swimming episodes induced by photoshock, when Chlamydomonas flagella beat with principal and reverse bends of similar magnitude, the central pair twists by 180 degrees between successive bends. These observations support a model in which central pair orientation in Chlamydomonas is linked to doublet-specific dynein activation, and bend propagation is linked to rotation of the central pair complex. Cell Motil. Cytoskeleton 56:120–129, 2003. © 2003 Wiley-Liss, Inc.