Supernumerary B chromosomes (Bs) represent a specific type of ‘selfish’ genetic element. As they are dispensable for normal growth, they generally show polymorphisms among populations. Marques et al. analyse the distribution and activity of B-located repeats in cultivated rye, Secale cereale subsp. cereale, and weedy relatives from seven countries ranging from Turkey to Japan and find that Bs maintain a similar molecular structure at the subspecies level. The high degree of conservation of the non-disjunction control region underlines its functional importance for the maintenance of B chromosomes. The conserved structure suggests that although rye Bs experienced rapid evolution including multiple rearrangements at the early evolutionary stages, this process has slowed significantly and may have even ceased during its recent evolution.