Gut microbiota impacts nearly every aspect of health, but researching it can be tricky due to differences between humans and commonly used model organisms, as well as interindividual variability in humans. A relatively new model, zebrafish have become a gold-standard model for biomedical research, and are especially used to study host-microbe interactions. In this article we will discuss zebrafish’s contribution to recent microbiota research and the features that make them particularly well-suited for studying the host-microbe interactions.