There are a number of pressing problems to understand in depth the various mechanisms underlying evolutionary processes of both animal and plant species. For instance, there are instances in which chromosomal rearrangements are not reflected in the morphology of a species. Holocarpha virgata of the Asteraceae family is a glaring example of this type. In a special issue Heredity [vol 108(1)] Professor Terence J Robinson at the University Stellenbosch, South Africa and Dr. F. Yang at The Wellcome Trust Sanger Institute, Cambridge, UK have elaborated on the effects of the interaction between molecular cytogenetics and comparative genomics in order to confirm and define syntenies, identify breakpoints, neocentromeres and other chromosomal features that contribute to the evolution of karyotypes – characteristic of biological lineages. Contributed by experts, the special number contains a number of papers that discuss chromosomal diversification at different phylogenetic levels. In conclusion the editor presents new and exciting insights to some of the molecular mechanisms considered to be responsible for the structural modification of karyotypes and the evolution of sex chromosomes and dosage compensation. New technologies now available with the molecular cytogenetics provide precision tools enabling researchers to identify accurately intricately structured chromosomal rearrangements and their role in elaborating phylogenetic relationships between the different phyla.