Northwestern Patagonia is inhabited by coastal dolphin species, including the Chilean (Cephalorhynchus eutropia) and Peale’s dolphin (Lagenorhynchus australis), which use habitats under contrasting anthropogenic pressures. To explore whether the skin bacteriome of Chilean and Peale’s dolphins reflects anthropogenic changes in their environment, we collected 122 skin biopsies, sequenced the V4 hypervariable region of the 16S rRNA gene, and investigated differences in the diversity, composition, and divergence of their bacterial communities across six different locations. Chilean and Peale’s dolphins from the highly anthropized locations showed a remarkably different composition of the skin bacteriome compared to dolphins from other locations, with a high relative abundance of Vibrio and Halomonas. The bacteriomes of dolphins from highly anthropized locations were highly similar, with low uniqueness. Such homogenization of skin bacteriomes between dolphins may be an early warning sign of deviations from optimal health. The skin bacteriome of Chilean and Peale’s dolphins proved to be a good indicator of the level of anthropization of their habitat.