Ecologically divergent, hybridizing species such as oaks and poplars provide models to identify genomic regions under selection and adaptive alleles that are transferred between species in hybrid zones. Oaks show patterns of genomic divergence characteristic for early stages of speciation with gene flow, in which large genomic regions are homogenized by interspecific gene flow interspersed by smaller regions (outlier regions) with high interspecific differentiation as result of divergent selection. These outlier regions can be identified using genome scans in hybrid zones and anchored to the Quercus robur genome sequence which will become available in the near future. Combined outlier and association genetic approaches can assess the role of individual genes in outlier genomic regions in adaptive trait variation. In contrast, hybridizing poplar species show a pattern of genomic divergence with large genomic regions of high interspecific differentiation punctuated by smaller regions of low differentiation as the result of interspecific gene flow. Genome scans in multiple hybrid zones of interfertile poplar species and in populations outside the area of sympatry will allow for the identification of genes that are exchanged between species by interspecific gene flow using the Populus trichocarpa genome sequence as a reference. Again association genetic approaches can be used for the characterization of variation in these introgressed genes with adaptive trait variation. In the present paper, the application of genomic approaches to identify genes for adaptive species divergence and reproductive isolation, and introgressed genes between species is discussed.