Ports and farms are well-known primary introduction hotspots for marine non-indigenous species (NIS). The extent to which these anthropogenic habitats are sustainable sources of propagules and influence the evolution of NIS in natural habitats was examined in the edible seaweed Undaria pinnatifida, native to Asia and introduced to Europe in the 1970s. Following its deliberate introduction 40 years ago along the French coast of the English Channel, this kelp is found in three contrasting habitat types: farms, marinas, and natural rocky reefs. In light of the continuous spread of this NIS, it is imperative to better understand the processes behind its sustainable establishment in the wild. In addition, developing effective management plans to curtail the spread of U. pinnatifida requires determining how the three types of populations interact with one another. In addition to an analysis using microsatellites, we developed, for the first time in a kelp, a ddRAD-sequencing technique to genotype 738 individuals sampled in 11 rocky reefs, 12 marinas, and 2 farms located along ca. 1000 km of coastline. As expected, the RAD-seq panel showed more power than the microsatellite panel for identifying fine-grained patterns. However, both panels demonstrated habitat-specific properties of the study populations. In particular, farms displayed very low genetic diversity and no inbreeding conversely to populations in marinas and natural rocky reefs. In addition, strong, but chaotic regional genetic structure, was revealed, consistent with human-mediated dispersal (e.g., leisure boating). We also uncovered a tight relationship between populations in rocky reefs and those in nearby marinas, but not with nearby farms, suggesting spill-over from marinas into the wild. Finally, a temporal survey (20 generations) showed that wild populations are self-sustaining, without local adaptation to any of the three habitats. These findings highlight that limiting the spread of U. pinnatifida requires management policies that also target marinas.