Genomes of higher plants contain a spectrum of repetitive DNAs elements, and during genome restructuring these elements can be evolutionarily highly dynamic. Jang et al. examine the evolution of a novel satellite DNA, PaB6, in the chromosomally variable monocotyledonous genus Prospero. Although present in all three species, PaB6 has undergone differential amplification only in the P. autumnale complex, particularly in cytotypes that have experienced chromosomal fusions and genome size increases. The PaB6 copy numbers are among the highest for repetitive elements of any higher plant, and their changes are exceptionally dynamic in this group of closely related cytotypes within a single species.