The microbiome is the name for the collection of microbes that live on or in another organism. The human microbiome has received a lot of attention, but in fact every living thing hosts a community of microbes that can be helpful—even vital—or sometimes harmful. In this study, we investigated the microbiome of tuna to identify the specific bacteria that populate it and whether the microbiome varies depending on the type of tuna, the ocean it lives in, or the organ. We found that the gut microbiome differs according to species due to feeding habits, while the skin microbiome differs according to the environment and is linked to the bacteria in the surrounding seawater. Bacteria that can cause food poisoning in humans were concentrated in the gut and liver of tuna, highlighting the importance of removing the organs before consuming this fish, which is one of the most widely eaten in the world.