Gene flow among populations of incipient species can act as a creative or destructive force in the speciation process. The flowering plant genus Carex exhibits a rapid and relatively recent radiation with many species limits still unclear. This is the case with the Iberian Peninsula (Spain and Portugal) endemic C. furva, which appears to be undergoing speciation. In the present study, we test how a young or incipient species is impacted by gene flow with its more widespread counterpart. We sampled the full range of distribution of C. furva and performed a morphological study, sequencing of two plastid DNA regions and genomic sequencing using restriction-site associated DNA sequencing (RADseq). We utilized divergence time analysis to date the divergence and a set of partitioned D-statistic tests to study the degree and direction of introgression. Morphological, plastid and nuclear genomic data all support the existence of two species, but intermediate morphology of some individuals in the south seem to be hybrids between the two species. This hybridization may be a result of a north-to-south long distance dispersal event or, more probably, expansions and contractions in the distribution during Quaternary glaciations. We conclude that secondary contacts are short-circuiting the speciation process of two incipient species.