Large marine vertebrates are important in marine ecosystems and can host a wide range of microorganisms. The microbiome is the full collection of genes of all microorganisms in a community, but often it is used as a term for all the microorganisms in a sample, not just their genes. Research that has been done in recent years shows that the microbiome had an impact on evolution of multicelular organisms. Moreover, it still plays an important role in normal functioning of digestive, integumentary and respiratory system. Large marine vertebrates include all marine mammals, several reptiles (seven species of marine turtles and one species of iguana) and cartilaginous fish (sharks and rays). Despite increasing amount of research, their microbiome has still not been sufficiently investigated. Gut microbiome of mammals and reptiles mostly consists of bacterial OTUs from phyla Bacteroidetes and Firmicutes, with less OTUs from phyla Proteobacteria, Fusobacteria and Actinobacteria. Bottlenose dolphin is (for now) the only mammal species that has significantly different microbiome from the rest of the mammals. Even though both mammals and reptiles show a correlation between gut microbiome and diet, the correlation is more pronounced among reptiles. When it comes to integumentary system, its health depends on the microbiome. All of the groups have genes specific for bacteria which produce antimicrobial substances. There is a possibility that these substances help maintain stable composition of skin microbiome or microbiome of turtle egg shells. The microbiome of respiratory system in mammals varies and there has not been any evidence of pathogen bacteria in healthy individuals. However, microbiome of this system is poorly researched and understood.