Spartina anglica arose during the end of the 19th century in England by hybridization between the indigenous Spartina maritima and the introduced East American Spartina alterniflora and following genome duplication of the hybrid (S. × townsendii). This system allows investigations of the early evolutionary changes that accompany stabilization of a new allopolyploid species in natural populations. Various molecular data indicate that S. anglica has resulted from a unique parental genotype. This young species contains two distinctly divergent homoeologous genomes that have not undergone extensive change since their reunion. No burst of retroelements has been encountered in the F1 hybrid or in the allopolyploid, suggesting a ‘structural genomic stasis’ rather than ‘rapid genomic changes’. However, modifications of the methylation patterns in the genomes of S. × townsendii and S. anglica indicate that in this system, epigenetic changes have followed both hybridization and polyploidization. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 82, 475–484.