Determining genetic connectivity of bottlenose dolphin communities helps identify evolutionary mechanisms, such as environmental and social factors, that interact to shape dispersal in highly social marine mammals. Here, we expand on a localized study that found marked genetic differentiation among resident dolphins (Tursiops aduncus) in the Port Stephens embayment and adjacent coastal communities, to include four additional communities inhabiting different environment types along the New South Wales coast, Southeastern Australia. Analysis of the mitochondrial DNA control region and seven microsatellite loci suggest the nine communities may have originated from a single ancestral population that progressively colonised the coast in a southward direction. Gene flow among communities was predominately governed by habitat type. The two enclosed embayments showed the highest level of genetic differentiation from other communities, while genetic differentiation among coastal and open embayment communities generally followed a pattern of isolation by distance. Directional bias in recent migration rates was evident, with the centrally located Hunter coast communities consisting of individuals with mixed ancestry from the Northern, Southern and Port Stephens communities. Emigration from Port Stephens was substantially higher than in the opposite direction, indicating there may be social barriers to dispersal created by Port Stephens dolphins. Our results suggest that the scale of connectivity of bottlenose dolphin communities inhabiting heterogeneous environments is likely to be affected by local habitat adaptation. This has important implications for the management of communities exposed to increasing levels of anthropogenic disturbances, such as the intensive commercial dolphin-watching industry operating in Port Stephens.