We present SyRI, an efficient tool for genome-wide identification of structural rearrangements (SR) from genome graphs, which are built up from pair-wise whole-genome alignments. Instead of searching for differences, SyRI starts by finding all co-linear regions between the genomes. As all remaining regions are SRs by definition, they can be classified as inversions, translocations, or duplications based on their positions in convoluted networks of repetitive alignments. Finally, SyRI reports local variations like SNPs and indels within syntenic and rearranged regions. We show SyRItextquoterights broad applicability to multiple species and genetically validate the presence of ~100 translocations identified in Arabidopsis.