Cytogenetics has played a key role in the history of scientific research in the Brassicaceae since the start of the last century. The discovery of the Brassica “U’s Triangle” species, elucidation of phylogenetic relationships and investigations of chromosome evolution all contributed to building up the basic genomic understanding of the Brassicaceae we have today. The advent of molecular cytogenetics in this family in the last 20 years has led to a progressively greater understanding of the factors underlying chromosome dynamics and organisation, meiotic and mitotic mechanisms and cell division processes. In addition, linking molecular cytogenetics with other molecular techniques, such as marker studies, DNA sequencing and protein expression analysis, has bridged the gap between chromosomes and linkage groups, resulting in a wealth of new information in this family. Future prospects for molecular cytogenetics in the Brassicaceae are bright. The recent and imminent release of additional Brassicaceae genomes will greatly facilitate development of probes for fluorescent in situ hybridisation as well as a comprehensive understanding of gene expression and protein interactions during cell division.