Despite the openness of the oceanic environment, limited dispersal and tight social structure often induce genetic structuring in marine organisms, even in large animals such as cetaceans. In the bottlenose dolphin, mitochondrial and nuclear DNA analyses have revealed the existence of genetic differentiation between pelagic (or offshore) and coastal (or nearshore) ecotypes in the western North Atlantic, as well as between coastal populations. Because previous studies concentrated on continental margins, we analysed the population structure of bottlenose dolphins in two of the most isolated archipelagos of the North Atlantic: the Azores and Madeira. We analysed 112 samples collected on live animals in the two archipelagos, and nine samples collected on stranded animals in Madeira and mainland Portugal. Genetic analyses consisted in molecular sexing, sequencing of part of the mitochondrial hyper-variable region, and screening of ten microsatellite loci. We predicted that: 1/ there is at least one pelagic and one or more coastal populations in each archipelago; 2/ populations are differentiated between and possibly within archipelagos. Contrary to these predictions, results indicated a lack of population structure in the study area. In addition, comparison with published sequences revealed that the samples from the Azores and Madeira were not significantly differentiated from samples of the pelagic population of the western North Atlantic. Thus, bottlenose dolphins occurring in the pelagic waters of the North Atlantic belong to a large oceanic population, which should be regarded as a single conservation unit. Unlike what is known for coastal populations, oceanic bottlenose dolphins are able to maintain high levels of gene flow.