The phenomena of chromoanagenesis have profoundly changed our conceptions regarding the genesis and etiology of complex rearrangements. These chaotic genomic events have also led to a better understanding of the mechanisms underlying the maintenance and fluctuations of genomic stability. Chromoanagenesis phenomena are now recognized as important drivers of karyotypic evolution, both in cancer and in developmental disorders. They question the conventional view of gradual evolution, supporting the role of genomic chaos in rapid evolutionary transitions. The advent of new genome sequencing technologies and their use in combination with powerful bioinformatics tools or single-cell analysis techniques have led to a better understanding of the complexity and heterogeneity of chromoanagenesis and to the description of new forms of complex and chaotic genomic rearrangements.