The family Orchidaceae is one of the largest plant family by the number of species and its taxonomy remains complex with frequent changes in nomenclate. New species are regularly described, some of them remaining difficult to identify, with few distinct morphological traits. Due to the evolution of the family, the species have been separated for a longer or shorter time leading to a more or less significant genetic differentiation between them. A similar situation can be observed within genera. Among these, the genus Epipactis, subfamily Epipendroideae, tribe Neottiae, which is widespread distributed in the Northern hemisphere is a good example. It consists of a variable number of species depending on the taxonomists. It includes a few well-differentiated species but also a large group of taxa whose distributions overlap, especially in Europe. Published phylogenies revealed weak differentiation between most species: nuclear genes, sequences of chloroplast genome and even a series of sequences obtained by RadSeq show similar results even if genomics was more powerful. The objectives of the present study of the genus Epipactis were (1) to develop new molecular markers suitable for building a comprehensive phylogeny based on nuclear genes, and (2) to analyse how polymorphisms maternally transmitted from chloroplast genome are shared between species and may reveal past hybridization. Data already obtained by comparing nuclear sequences produced by RNAseq from three different plants are suitable for finding polymorphic regions in expressed sequences. Among the numerous sequences, 500 were selected, on the basis of their polymorphisms and homologies with sequences from other genera of the subfamily Epidendroideae. Some sequences lent themselves for phylogenetic analysis. In addition, DNA fragments amplified as SRAP markers are used in the same large sample of species. The clear differentiation of section Arthrochilium, represented in Western Europe by E. palustris, is confirmed. Species in the E. helleborine group are much less differentiated. Analysis of new data from chloroplast genome (matK, intergene between trnL and trnF) reveals a sharing of sequence between plants of different species and stands. There is evidence of past hybridizations and migrations of introgressed lineages. The controversal presence of E. lusitanica in France could be documented and theses plants resulted probably from a lineage introgressed by E. tremolsii as female parent. The recent radiation of genus Epipactis has resulted in different taxa with overlapping distribution, not yet genetically separated and still able to hybridize.