Abstract
<title>Abstract</title> <p> Habitat fragmentation and the disruption of river connectivity threaten the long-term persistence of riparian species by reducing gene flow, increasing inbreeding, and eroding genetic diversity. <italic>Myricaria germanica</italic> , a pioneer shrub once widespread throughout European river systems but now largely confined to fragmented headwater populations, provides an excellent model for investigating how historical and contemporary processes shape genetic diversity and connectivity in threatened riparian plants. We analyzed genetic diversity, population structure, and migration across 67 populations from 12 Central European river catchments using 20 nuclear and six chloroplast microsatellite loci, enabling comparisons of pollen- and seed-mediated gene flow across contemporary and historical timescales. Both marker systems revealed low genetic diversity, high inbreeding, and strong population differentiation, indicating pronounced genetic subdivision throughout the species' range. Gene flow was highly asymmetric among catchments, with the Tagliamento acting as a major genetic sink, the Rhine serving as a regional connectivity hub, and the Po exhibiting more balanced genetic exchange. Nuclear markers revealed widespread and relatively symmetrical gene flow, consistent with extensive pollen-mediated connectivity and historical long-distance seed dispersal, whereas chloroplast markers showed limited and directional gene flow, reflecting restricted seed dispersal. Contemporary migration analyses further indicated that seed-mediated gene flow is now largely confined within individual catchments despite evidence of broader historical connectivity. Together, these findings support a two-phase postglacial colonization scenario involving rare long-distance seed dispersal during range expansion, followed by prolonged pollen-mediated gene flow. The marked genetic differentiation among catchments and the limited contemporary dispersal indicate that individual river catchments represent biologically meaningful conservation units that harbor unique components of the species' genetic diversity. Overall, our results demonstrate that <italic>M. germanica</italic> retains clear signatures of historical connectivity but is undergoing increasing contemporary genetic isolation. These findings underscore the importance of maintaining river connectivity, prioritizing genetically important catchments such as the Rhine and Tagliamento, and preserving the evolutionary potential of this threatened riparian species. </p>