Increasing depletion of fish stocks in the Mediterranean Sea intensifies conflicts between fisheries and marine mammals, such as the common bottlenose dolphin (Tursiops truncatus, Montagu, 1821). To increase the knowledge of such interactions in the eastern Mediterranean Sea, fishing activities of commercial fisheries and biomass of fish families targeted by fisheries and T. truncatus were analysed to identify areas that are more likely to be affected by these conflicts in the Dodecanese region of Greece. The area with the highest risk of conflict is located between Kos and Leros islands and the southwest coast of Turkey, which is mainly caused by trawl fishing activities. The presence of Sparidae, Merlucciidae, Mullidae and other unspecified fish families increased the likelihood of conflicts. Our applied method and results can be used to improve fishing regulations and management to diminish similar conflicts elsewhere in the world.