Genus Spartina is composed of polyploid perennial plants colonizing salt marshes. Spartina species play an important ecological role in the salt marsh dynamics where they are considered as “ecosystem engineers”. Polyploidy (from tetraploid to dodecaploid levels) and hybridisation are recurrent in this genus, where they represent central mechanisms to diversification and adaptation, and thus offer an excellent opportunity to explore the genomic consequences of genome merger and genome duplication at various evolutionary time scales. We are particularly interested in the recent formation of the allo-dodecaploid Spartina anglica that has now invaded several continents, following introduction of the American hexaploid S. alterniflora to Western Europe and its hybridisation with the native hexaploid S. maritima. In an effort to develop genomic resources in this system, we used massive parallel sequencing of the genomes and transcriptomes of the hexaploid parental species. Our results provide the first evaluation of the genic and repetitive components of these previously poorly-investigated genomes. Spartina genes from different tissues were identified and annotated, in the perspective of examining expression evolution of ecologically important genes following allopolyploid speciation. The relative importance of repetitive sequences (e.g. transposable element families, ribosomal genes) was evaluated in the hexaploid parent S. maritima.