Human activities have deeply transformed the Mediterranean landscape for millennia. Wetland and riverbed vegetation are among the most affected ecosystems because of the value of these areas for agriculture, due to their rich soil and water availability. This has caused the fragmentation, population reduction, and extinction of many species. We focus our study on Ulmus laevis Pallas, an endangered tree species in the Iberian Peninsula, as an extreme example of these formations. We study the diversity and fine-scale spatial genetic structure of two human disturbed wetland populations with chloroplast markers and nuclear microsatellites. We evaluate their recovery possibilities, and how they will be affected by future aridification and water table depletion. Our results show that although these populations have suffered bottlenecks and have low genetic diversity, they maintain the same diversity levels as the European populations. Despite the low genetic variation that could contribute to inbreeding problems in the future, we discuss that the main threat of the species is habitat destruction. Finally, we propose some management and conservation policies to ameliorate these effects.