In rabbits, the bacterial and archaeal community of caecal ecosystem is composed mostly of species not yet described and very specific to that species. In mammals, the digestive ecosystem plays important physiological roles: hydrolysis and fermentation of nutrients, immune system regulation, angiogenesis, gut development and acting as a barrier against pathogens. Understanding the functioning of the digestive ecosystem and how to control its functional and specific diversity is a priority, as this could provide new strategies to improve the resistance of the young rabbit to digestive disorders and improve feed efficiency. This review first recalls some facts about the specificity of rabbit digestive microbiota composition in the main fermentation compartment, and its variability with some new insights based on recent molecular approaches. The main functions of the digestive microbiota will then be explained. Finally, some possible ways to control rabbit caecal microbiota will be proposed and a suitable timing for action will be defined.