Marine mammals serve as sentinels of ocean health but little attention has been paid towards their microbiota. Here I will describe our efforts to explore and understand patterns within the microbiomes associated with the skin, respiratory blow and entire gastrointestinal tract of humpback, bowhead and North Atlantic right whales. I will share new knowledge about the biodiversity of these environments, prominent microbial species and understandings of how these microbiomes vary with animal traits and ocean habitats.