Although the first description of chromosomes of Arabidopsis dates as far back as 1907, little attention was paid to its cytogenetics for a long time. The spectacular interest in chromosome research for this species that now is the model plant species by excellence came with the introduction of molecular cytogenetical research including FISH technology, genome sequence data and immunodetection of chromatin proteins. In this paper, we present an overview of the most important cytogenetic tools that were developed for Arabidopsis in recent decades. It shows the power of meiosis for studying synaptic mutants and FISH technology, and the development of numerical and structural chromosome mutant series like trisomics, telotrisomics and translocations for assigning linkage groups to chromosomes. Its small genome and chromosome size and relatively simple organization of heterochromatin have been the key to a successful characterization of the molecular organization of repetitive and single copy sequences on the chromosomes, both in metaphase and pachytene complements, but also in interphase nuclei and extended DNA fibres. Finally, Arabidopsis is the first plant species in which a heterochromatin knob could be analysed in full detail and in which chromosome painting with BAC clones covering whole chromosome arms could be established. All these achievements are probably only the very first steps in a promising new era in plant cytogenetics and chromatin research yet to come.