Abrupt speciation through interspecific hybridisation is an important mechanism in angiosperm evolution. Flowering plants therefore offer excellent opportunities for studying genetic processes associated with hybrid speciation. Novel molecular approaches are now available to examine these processes at the level of both genome organization and gene expression - transcriptomics. Here, we present an overview of the molecular technologies currently used to study hybrid speciation and how they are providing new insights into this mode of speciation in flowering plants. We begin with an introduction to hybrid speciation in plants, followed by a review of techniques, such as isozymes and other markers, which have been used to study hybrid species in the past. We then review advances in molecular techniques that have the potential to be applied to studies of hybrid species, followed by an overview of the main genomic and transcriptomic changes suspected, or known, to occur in newly formed hybrids, together with commentary on the application of advanced molecular tools to studying these changes.