Scrophularia arguta (Scrophulariaceae) is a rare amphicarpic annual species with a fragmented distribution in North Africa, part of the Arabian Peninsula, and Macaronesia, with several peripheral populations on the Iberian Peninsula (south-western Europe) as well. The Iberian populations have a disjunct distribution: several endangered or critically endangered populations are present in the southeast versus a few non-listed ones representing a relict lineage with a unique plastid haplotype inhabiting the west-central region (Extremadura). In this study, we examined the largest and most important population of this relict lineage to assess potential threats to its survival. We evaluated pollination and reproductive systems, floral rewards, fruit and seed set from chasmogamous and cleistogamous flowers, and population dynamics (i.e., phenology, survival, reproductive success, and predation level). We found that the main threats to the population are predation by wild herbivores, such as red deer and, to a lesser extent, Cucullia scrophulariae caterpillars. These threats decrease reproductive success to such an extent that population survival may be in jeopardy if no action is taken to reduce the effects of herbivores. In addition, the existence of nearby beehives alters the presence and density of wild pollinators that contribute to gene flow via pollen transfer and increase genetic variability. Cleistogamous seeds may help maintain the population in specific microhabitats (mainly quartzite rock cracks), although at the cost of reducing genetic variability. Finally, we recommend that regional/national administrations responsible for biodiversity matters adopt measures to ensure the conservation and survival of west-central populations. Scrophularia arguta predation by vertebrates. Left, group of several individuals before and after vertebrate predation. Right, vertebrate predation level. • Wild vertebrates and caterpillars threaten a relict Scrophularia arguta population. • Managed honeybees displace natural pollinators. • The conflict between plant and animal conservation requires monitoring. • The action of regional/national administrations is needed to conserve this species.