AbstractIn this paper, we propose a method for computing partial functional correspondence between non‐rigid shapes. We use perturbation analysis to show how removal of shape parts changes the Laplace–Beltrami eigenfunctions, and exploit it as a prior on the spectral representation of the correspondence. Corresponding parts are optimization variables in our problem and are used to weight the functional correspondence; we are looking for the largest and most regular (in the Mumford–Shah sense) parts that minimize correspondence distortion. We show that our approach can cope with very challenging correspondence settings.