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Motion capture (mocap) data normally used to produce a three-dimensional (3D) mesh animation is exploited for watermarking. Copyright protection of the 3D mesh animation obtained is not guaranteed since identical joints in the mocap data are not distinguished easily. A novel robust blind watermarking method is proposed for the copyright protection of 3D mesh animations in the paper. At the beginning, the shape diameter function (SDF) method segments one frame of a 3D animation into several meaningful parts. A watermark is then embedded into these parts by adjusting the geodesic distances. Vertex trajectories are further exploited to modify the geodesic distribution of residual frames to be the same as that of the watermarked frame. Our experimental result demonstrates that the proposed method is able to resist the noise addition, similarity transformation, quantization, cropping, simplification, smoothing, and resampling attacks.