The diversity of species in a given ecosystem, which contributes to biodiversity, can be maintained if they are reproductively isolated from each other. This ensures the genetic and phenotypic distinctiveness between species, which also allows new species to arise, namely speciation. Therefore, understanding speciation mechanisms requires unraveling the genetic elements causing reproductive isolation. Within the Capsella genus, C. rubella and C. grandiflora diverged about 100,000 years ago. Despite this recent divergence, we demonstrated that C. rubella × C. grandiflora hybrid seeds barely survive, revealing a strong postzygotic reproductive barrier between the two species. Our first genetic data suggest that this hybrid incompatibility follows a Bateson-Dobzhansky-Muller model, with three paternal C. grandiflora negatively interacting with one C. rubella locus to impair hybrid seed viability. To locate these loci and identify their functions, we plan to follow a ddRAD-tag multiplex sequencing strategy to generate sufficient markers to identify QTLs and genes underlying these QTLs.