Population substructure has important implications for a species' ecology and evolution. As such, knowledge of this structuring is critical for the conservation and management of natural populations. Among marine mammals, many examples exist of species that enjoy a broad geographical distribution, yet are characterized by fine-scale population subdivisions. Coastal bottlenose dolphins have been studied extensively in a few regions globally, and these studies have highlighted a great diversity in both social strategies and demographic isolation. Here we use molecular genetic markers to examine the degree of population subdivision among three study sites separated by less than 250 km on Little Bahama Bank in the northern Bahamas. Mitochondrial DNA (mtDNA) sequence variation and microsatellite genotypes were used to assess partitioning of genetic variance among 56 individually recognized coastal ecotype bottlenose dolphins. Although resolved levels of genetic differentiation suggest gene flow among the three study sites, both nuclear and mitochondrial data indicate a significant degree of subdivision within the Little Bahama Bank population, and sex-based analyses suggest that patterns of dispersal may not be strictly biased toward males. These results corroborate the site fidelity documented through long-term photo-identification studies in the NE Bahamas, and highlight the need to consider independent subpopulation units for the conservation and management of coastal bottlenose dolphins in the Bahamas.