Vessel traffic is one of the major sources of underwater anthropogenic noise. Dolphins can modify their vocal repertoire, especially whistles, in presence of vessels to facilitate their communication. Acoustic data were collected (sampling rate 96 kHz) in La Paz Bay, Gulf of California, Mexico. Whistle rate and parameters of the coastal and oceanic ecotypes of common bottlenose dolphins (Tursiops truncatus) were measured in absence of vessels and in presence of moving small vessels (size 5–10 m). The peak noise difference was calculated between the two frequency bands dominated by the whistles (2000–20,000 Hz) and the small vessel (500–2000 Hz). In presence of vessels the oceanic ecotype decreased whistle frequencies while the coastal ecotype increased them. Both ecotypes raised whistle frequencies with the decreasing of the peak noise difference. The differences in habitat and group structure could have driven the two ecotypes to react in a different way to the vessel presence.