Background <p><i>Scrophularia oxyrhyncha</i> (Scrophulariaceae), endemic to southwest Spain, is one of the species of the genus whose distribution across the Iberian Peninsula is most limited. In this study, we analyzed its reproductive system by evaluating its fruit and seed set after different treatments, floral phenology, reproductive success, and the predation level of two populations in the Extremadura region (Spain), inhabiting different substrates (quartzitic in the San Serván population, granitic in the Cornalvo population) between 2019 and 2022.</p> Results <p><i>Scrophularia oxyrhyncha</i> presents protogyny, it is self-compatible but requires the presence of pollinators to produce offspring which, in quite a high percentage, would result from geitonogamous pollinations. The two populations did not differ significantly in their reproductive behaviour throughout the years studied, and both presented a spring synchronous pattern, somewhat longer in the San Serván population; this was probably due to the existence of two short second flowering periods caused by sheep predation suffered by individuals. The main threat to the populations was cattle grazing and, to a lesser extent, caterpillars.</p> Conclusions <p>Cattle grazing decreased reproductive success and altered the floral display in such a way that there was a flowering time-pollinator activity mismatch. The decline in reproductive success due to vertebrate predation depended on the time at which such predation occurred, with the most severe being late predation, that is, after peak flowering. Finally, we recommend that the pertinent authorities adopt measures to ensure the conservation and survival of the populations of this endemic species in Extremadura.</p>