The cultivation of macroalgae for biofuels, food and fertilisers has increased dramatically in recent years. The demand for such algal-derived products means that large scale cultivation in coastal waters will become necessary to provide sufficient algal biomass. As part of the process of establishing new macroalgal farms, the potential for gene flow between cultivated specimens and natural populations needs to be taken into consideration. Consequently, in the present study we have used a combined population genetic and hydrodynamic modelling approach to determine potential levels and patterns of gene flow in the kelp Saccharina latissima. Microsatellite analysis of 14 populations sampled across the northern part of the Irish Sea indicated four distinct genetic clusters. These were consistent with dispersal patterns indicated by the particle tracking model and show a combination of isolation by distance and genetic structuring due to local hydrodynamic conditions. At smaller scales (less than a few 10s of km), gene flow appears to be fairly extensive, with evidence of local population connectivity due to local currents. At larger scales, however, factors such as freshwater efflux and open water would appear to represent barriers to gene flow. Together, these patterns suggest that factors other than simple geographical distance and proximity need to be taken into account when planning the siting of kelp farms with the aim of minimizing gene flow to and from natural populations.