Nucleolar dominance is an enigma. The puzzle of differential amphiplasty has remained unresolved since it was first recognised and described in Crepis hybrids by Navashin in 1934. Here we review the body of knowledge that has grown out of the many models that have tried to find the genetic basis for differential rRNA gene expression in hybrids, and present a new interpretation. We propose and discuss a chromatin imprinting model which re-interprets differential amphiplasty in terms of two genomes of differing size occupying a common space within the nucleus, and with heterochromatin as a key player in the scenario. Difference in size between two parental genomes induces an inherited epigenetic mark in the hybrid that allows patterns of chromatin organization to have positional effects on the neighbouring domains. This chromatin imprinting model can be also used to explain complex genomic interactions which transcend