Marine mammals are globally significant because of their sensitivity to environmental change and threatened status, often serving as ‘ecosystem sentinels’. Disease is a major cause of marine mammal population decline and the role of the microbiome in disease has generated considerable interest. Recent research in humans has greatly enhanced our understanding of how the host-associated microbial community, the microbiome, affects host health. In this review, we provide an overview of the extent of the marine mammal microbiome with a focus on whole community characterisation using genomic methods. This research highlights the overlap in microbial communities between geographically distinct species and populations of marine mammals, suggesting tight links between marine mammals and their microbial symbionts over millions of years of evolution. An understanding of these links in both healthy and compromised hosts is essential to identifying at-risk populations and making ecologically appropriate management decisions. We advocate further development of innovative sampling and analytic techniques that advance the field of microbial ecology of marine mammals.