River regulation has profoundly altered hydrological regimes in alpine floodplains, leading to severe habitat loss and population declines of specialist species such as Myricaria germanica. Since the early 2000s, extensive reintroduction programs have been implemented to counteract the consequences of channelization and embankment, aiming to prevent the extinction of this characteristic gravel-bank shrub. Yet, the genetic outcomes of these measures remain largely unexplored, while the potential influence of founder and bottleneck effects on restoration success remains uncertain. We analyzed genetic variation within and among natural and restored populations along the rivers Isar and Lech in southern Germany and northern Austria. Restored populations exhibited genetic diversity comparable to natural populations along the Isar, and differentiation between seed source and restored sites was modest (PhiPT = 0.12). Our findings show that restoration relying on a single, genetically variable source population can successfully maintain local genetic diversity. This highlights that targeted reintroduction can safeguard genetic variation while avoiding possible long-term risks of excessive mixing, such as potential outbreeding depression or reduced fitness, thereby supporting the persistence of this iconic riverine species under ongoing environmental change.