The concept of the ‘nucleotype’ embraces aspects of the nuclear DNA that affect the phenotype other than through the coding sequences. In this context, we consider one particular situation, namely DNA variation due to the presence of supernumerary B chromosomes (Bs); these Bs, which are additional to the basic complement of A chromosomes, generate a spectrum of DNA amounts, and thus nucleotypes, within many species. We consider the physiological consequences of carrying extra chromosomes that appear by and large to lack coding sequences, and focus on two species with contrasting case histories: rye (Secale cereale L.) and chives (Allium schoenoprasum L.), which illustrate ‘selfish’ and ‘adaptive’ explanations of the persistence of B chromosomes.