Whistle characteristics were quantitatively compared between both geographically separated and neighboring populations of Atlantic spotted dolphins (Stenella frontalis), bottlenose dolphins (Tursiops truncatus), and pilot whales (Globicephala spp.) in U.S. waters to evaluate if intraspecific acoustic differences exist between groups. We compared nine whistle characteristics between continental shelf and offshore Atlantic spotted dolphins in the western North Atlantic and between northern Gulf of Mexico and western North Atlantic bottlenose dolphins and pilot whales using discriminant analysis. Offshore Atlantic spotted dolphin whistles were significantly different (Hotelling's T2, P= 0.0003) from continental shelf whistles in high frequency, bandwidth, duration, number of steps, and number of inflection points. Atlantic bottlenose dolphin whistles were significantly different (Hotelling's T2, P < 0.0001) from those in the Gulf of Mexico in duration, number of steps, and number of inflection points. There was no significant difference between pilot whale whistles in the two basins. The whistle differences indicate acoustic divergence between groups in different areas that may arise from geographic isolation or habitat separation between neighboring but genetically distinct populations of dolphins. This study supports the premise that acoustic differences can be a tool to evaluate the ecological separation between marine mammal groups in field studies.