show Abstracthide AbstractClosely related hybridizing species represent a unique opportunity to raise information on the speciation process. In such systems, local adaptation to contrasting conditions can lead to speciation by either reducing mating possibilities between phenotypically divergent lineages or by decreasing hybrids' performance. In this project, we aim at investigating the importance of adaptive mechanisms for the speciation of Epidendrum fulgens and E. puniceoluteum. Moreover, we aim to evaluate the importance of adaptive introgression in genes associated with tolerance to high levels of salinity, flooding, and lack of soil nutrients for the species survival in the restingas. Epidendrum fulgens and E. puniceoluteum are closely related species, associated with contrasting adjacent habitats, that hybridize in the restingas in southern and southeastern Brazil. We employed genomic data from RNA sequencing (RNA-seq) to investigate the genomic basis of the adaptation and speciation process between these species. Although the Tropics harbor most part of biodiversity, we still lack information on the role of selection in the speciation processes and we depend on the emergence of model groups in which previous ecological and genetic information might guide sampling design and hypotheses formulation. Investigating the speciation in this group will be fundamental to improve our understanding of the role of natural selection in the origin of neotropical species and on the mechanisms underlying the evolution and maintenance of reproductive barriers between species despite interspecific gene flow.