Plants have played a significant role in the discovery of inheritance principles and many biological phenomena, such as the chromosomal basis of inheritance, the genome dynamics conferred by transposable elements, or the evolutionary implications of chromosomal mutations. While the molecular basis of gene structure and function has been widely studied, many aspects of chromosome structure, its functional significance and evolutionary implications remain to be established. This special issue of Cytogenetic and Genome Research presents an excellent compilation of current research in a wide range of cultivated and wild plant species. The contributions, reviews as well as original articles by experts in the field, reflect representative aspects of nuclear and chromosome organization, behavior in somatic and germ cells, evolution, and manipulation in breeding programs. It is an excellent source of information for investigators and students in plant genetics, plant biology and agronomy.