The identification of localized discrete populations is particularly important to the management and conservation of animal species, especially in the marine environment, where potential for dispersal is high but barriers to gene flow are often not clear. We investigated population genetic structuring of bottlenose dolphins Tursiops truncatus found along the west coast of Ireland, with particular attention to the Shannon Estuary, which is the only candidate Special Area of Conservation designated for this species in Irish waters. A genetic structure analysis using 62 biopsy samples from free ranging dolphins and 23 necropsies from stranded dolphins revealed fine-scale population structure among three distinct populations. The Shannon Estuary population appears to be genetically isolated from adjacent coastal areas, with the exception of four animals sampled from a small group of six dolphins that are now resident in Cork Harbour (south coast) indicating ongoing gene flow or recent dispersal between these two areas. A second genetically distinct aggregation was identified in the Connemara–Mayo region, where recent photo-identification studies have suggested that dolphins found in this area show a degree of site fidelity. We found moderate nuclear (15 microsatellites) and low mitochondrial (544 bp of the control region) gene diversity in dolphins using the Shannon Estuary and the Connemara–Mayo region, while dolphins that stranded along the coast showed markedly higher levels of gene diversity at both classes of markers. Specifically, these stranded dolphins formed a third genetically distinct cluster, which may be part of a larger pelagic population, as also suggested by the high levels of gene diversity. These results provide new insights into population structure of bottlenose dolphins in Irish waters and will aid future management and conservation of the species in the eastern North Atlantic.