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BackgroundGypsum ecosystems are edaphic islands surrounded by a matrix that is inhospitable to gypsum soil plant specialists. These naturally fragmented landscapes are currently exacerbated due to man-made disturbances, jeopardising their valuable biodiversity. Concomitant action of other fragmentation drivers such as linear infrastructures may increase the already high threat to these specialists. Although some evidence suggest that gypsophytes are not evolutionary dead-ends and can respond to fragmentation by means of phenotypic plasticity, the simultaneous action of barriers to genetic flow can pose a severe hazard to their viability. Here, we evaluated the effect of a highway with heavy traffic on the genetic flow and diversity in the speciesLepidium subulatum, a dominant Iberian shrubby gypsophyte.MethodsWe tested the possible existence of bottlenecks, and estimated the genetic diversity, gene flow and genetic structure in the remnant populations, exploring in detail the effect of a highway as a possible barrier.ResultsResults showed variability in genetic diversity, migrants and structure. The highway had a low impact on the species since populations can retain high levels of genetic diversity and genetic parameter, likeFSTandFIS, did not seem to be affected. The presence of some level of genetic flow in both sides along the highway could explain the relatively high genetic diversity in the habitat remnants.DiscussionNatural fragmentation and their exacerbation by agriculture and linear infrastructures seem to be negligible for this species and do not limit its viability. The biological features, demographic dynamics and population structures of gypsum species seem to be a valuable, adaptive pre-requisite to be a soil specialist and to maintain its competitiveness with other species in such adverse stressful conditions.