The meaning of ‘biodiversity’ ranges from genetic makeups to communities, covering almost all biological phenomena, still remaining linked to species diversity. Ecosystems function through three basic cycles of matter and energy: extraspecific cycles (biogeochemical cycles), intraspecific cycles (life cycles and histories), and interspecific cycles (food webs). In an evolutionary framework, ecology is characterised by change: evolutionary processes never stop. Change is either structural or functional, or both. Palaeontology and long-term ecological series show that stable ecosystems do not exist, at least in structure. In non-linear systems like environmental ones, even small changes in biodiversity can cause sharp changes in ecosystem functioning, changing the shape of environmental attractors. The currently accepted definition of ecosystem functioning (the efficiency of biogeochemical cycles) is insufficient to account for ecosystem health. The efficiency of extra-, intra- and interspecific cycles must be taken into consideration in order to know ‘who does what’. To account for the historical nature of ecological phenomena, the Historical Biodiversity Index is proposed, considering not only the present status of a given habitat type (in terms of species composition) but also its history. This will allow biodiversity crises to be identified, including potential extinction. Natural history and experimental ecology must cooperate to help untangle ecological complexity, merging biodiversity with the functioning of ecological systems.