Elucidating biological barriers to connectivity, such as predation pressure, is helpful for understanding the processes of marine dispersal. Many marine protected areas (MPAs) have been advocated around the world. Their establishment often causes contrasting predation pressures between MPAs and fishing zones, enabling to test the top-down impacts on marine dispersal. We examined the differences in the abundance, immigration and self-recruit production rates between the two zones by using a field survey and genetic parentage analysis for two anemonefishes (Amphiprion frenatus and A. perideraion). We found lower abundance level of the two anemonefishes in the MPA than in the fishing zone. Parentage analysis also showed lower immigration rates from the fishing zone into the MPA than those into the fishing zone. Stronger top-down control in the MPA was the most plausible explanation for such patterns. Our results highlighted the importance of top-down effects as a factor influencing connectivity.