Undaria pinnatifida, a kelp species native to East Asia, has become cosmopolitan and drawn increasing attention due to its worldwide spread in recent decades. Floating fragments of this alga were found washed ashore on Sylt in 2016, the first record of this species in Germany. Thalli attached to local oyster reefs were detected in 2017. The genetic relationship between the floating and attached thalli on Sylt, as well as their relevance to the populations from northern Europe and native regions, was hitherto unknown. Here, 10 microsatellite markers were used to assess relationships between the recently established population on Sylt and five other northern European populations in France (Brittany, West English Channel), the Netherlands and England (Plymouth, West English Channel) plus three natural populations in China. Almost no genetic differentiation was detected between the floating and attached populations on Sylt, but they were genetically distinct from all the other studied northern European populations. The very low genetic diversity revealed in the new founder populations of Sylt suggests that they came from genetically similar parents. The marked reduction in both the number of alleles and heterozygosity in the northern European populations, as compared with the Chinese ones, is typical of founder effects in recently populated regions. Prominent genetic divergence was found between most of the northern European populations except those within Brittany and Sylt. Further studies will focus on identifying the putative source populations that might be found on shellfish farms, in local marinas or the benthic habitats around Sylt Island.