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This special issue reflects the intersection between molecular cytogenetics and comparative genomics and emphasizes their use to confirm and refine syntenies, identify breakpoints, neocentromeres and other chromosomal features that are responsible for the myriad of karyotypes that characterize biological lineages. It features papers that discuss chromosomal diversification at different phylogenetic levels and presents new and exciting insights to some of the molecular mechanisms that are thought to underpin the structural modification of karyotypes (including the evolution of sex chromosomes and dosage compensation in amniotes), and new technologies that may impact on the precision by which we identify and characterize chromosomal rearrangements in future.