We propose a spectral partitioning approach for large-scale optimization problems, specifically structure from motion. In structure from motion, partitioning methods reduce the problem into smaller and better conditioned subproblems which can be efficiently optimized. Our partitioning method uses only the Hessian of the reprojection error and its eigenvector. We show that partitioned systems that preserve the eigenvectors corresponding to small eigenvalues result in lower residual error when optimized. We create partitions by clustering the entries of the eigenvectors of the Hessian corresponding to small eigenvalues. This is a more general technique than relying on domain knowledge and heuristics such as bottom-up structure from motion approaches. Simultaneously, it takes advantage of more information than generic matrix partitioning algorithms.