Speciation is the only process that can generate biodiversity, but a holistic view of factors that drive this process is lacking. In sexually reproducing organisms, speciation can be viewed as the build-up of reproductive isolation. In the final stages of this process, reproductive isolation becomes complete as genetic incompatibilities between the emerging young species make their hybrids sterile or inviable. The Dobzhansky-Muller (DM) model assumes that genetic incompatibilities are caused by negative epistatic interactions between alleles, which have not jointly been exposed to selection in the past. However, the current empirical knowledge on genetic incompatibilities is largely limited to studies based on laboratory model species such as Drosophila. This limitation hampers a holistic view of the factors that actually drives speciation (i.e. the evolution of the genes causing incompatibilities). We study a natural hybrid zone of collared and pied flycatchers and have found clear signatures of genetic incompatibilities in the form of male hybrids having malformed sperm and reduced fertility. Spermatogenesis is one of the most complex processes of cellular differentiation having multiple steps of cell division and cell transformation. In this study we use the latest state of the art RNA single sequencing techniques to unveil the different cell types and transcriptomic profiles of the spermatogenesis process in both pure species and hybrid flycatchers with the aim to identify possible candidates for genetic incompatibilities. The ultimate goal being to increase our understanding of the relative roles of mechanisms behind the divergence of these particular genes, in other words of genetic drift, natural and sexual selection/sexual conflict and meoitic drive.