Several previous studies have reported high levels of genetic differentiation between populations inside European Marine Reserves and their adjacent coastlines for a direct-developing species. These studies suggest that sea loughs may not represent the most suitable sites for inclusion into Marine Protected Area (MPA) or Marine Reserve networks as they are not well connected to other populations. However, many marine species have pelagic larvae, and the connectivity of populations of such species inside sea loughs with non-lough populations remains unknown. Here, I investigated the levels of gene flow between populations of the acorn barnacle Semibalanas balanoides inside and outside Strangford Lough, Northern Ireland; this species has a long-lived pelagic larvae (4–6 weeks). There were no significant differences in the levels of genetic diversity between sea lough and non-lough populations and no evidence for genetic differentiation between any of the populations examined; the populations appear well mixed and well connected, in contrast to what has been reported for a previous direct-developing species.