The plant nucleus is a highly ordered and dynamic structure, with a considerable level of variation between species in terms of genome size, genome organisation, chromosome territories and patterns associated with developmental changes. Diploids naturally represent the simplest state of affairs, but in the plant world more than 70% of species may have been involved in polyploidisation events at some stage during their evolution. Autopolyploids have multiple sets of chromosomes from a single species, and aside from the complexities of meiosis we may expect them to accommodate their polysomic state as well as their disomic relatives. Allopolyploids are at the other extreme, with multiple sets of chromosomes from 2 or more species, embedded in the cytoplasm of the maternal parent following hybridisation, and this presents the nucleus of nascent allopolyploids with certain zones of conflict. Nature has found ways to make the accommodation, and recent developments in molecular analysis have now opened a window for the experimenter to view the process of this adjustment, and to see how rapidly it takes place and what processes are involved. The nature of the resolution of nuclear conflicts in diploid hybrids and in allopolyploids is discussed.