The gastrointestinal tract of the adult human represents the habitat of the ecological community of commensal, symbiotic and pathogenic microorganisms, defined as the gut microbiota, which has more than 100 trillion microorganisms representing one of the most complex ecosystems. Colonization of the gastrointestinal tract by microorganisms begins at the time of birth. Contrary to what was previously hypothesized, a large number of fundamental functions for the host are attributed to the gut microbiota to date. The gut microbiota, therefore, does not represent a passive set of microbes hosted inside the human organism but plays a crucial role in the balance of the organism itself. An alteration of the microbiota is a phenomenon known as dysbiosis. The latter can be implicated in the development of complex liver diseases like non-alcoholic fatty liver disease. The aim of this review is to describe the most interesting data linking the development of non-alcoholic fatty liver disease with the gut microbiota and, therefore, to underline the importance of the microbiota itself, as a potential therapeutic target in the treatment of non-alcoholic fatty liver disease.