Hybridization and polyploidization are now recognized as major phenomena in the evolution of plants, promoting genetic diversity, adaptive radiation and speciation. New findings suggest that the interactions of the combined genomes in allopolyploids induce waves of genetic and epigenetic alterations that have the potential to result in novel expression patterns and new phenotypes.Such novelties, in combination with heterosis and gene redundancy, might confer on hybrids an elevated evolutionary potential. Hybridization has the potential to occur repeatedly between different populations of the same parental taxa, leading to arrays of allopolyploids that subsequently interbreed.This is the case also in the Dactylorhiza incarnata/maculata complex, e.g., for the allotetraploid pair D. traunsteineri and D. majalis s.s., which both resulted from hybridization of D. fuchsii and D. incarnata.To further our understanding on the consequences of hybridization and genome duplication on polyploid genome natural evolution and adaptation to the environment, I propose here the use of this allotetraploid pair with similar genetic background, but difference in their evolutionary history and ecology: D. traunsteineri is a recently formed, morphologically variable hybrid with a narrower distribution and D. majalis s.s. has a wider distribution and is much more uniform morphologically.A cDNA amplified fragment length polymorphism (AFLP) genome-wide survey of the transcriptome, together with a methylation sensitive AFLP approach is expected to indicate the functional relevance of correlations between gene expression and the development of a phenotype, the direction and stochastic nature of the diploidization process, and the molecular mechanisms that result in adaptation to different habitats and therefore in reproductive isolation.The methods proposed are among the most modern and advanced strategies to provide inferences on the principle of genomic responses to allopolyploidization.