Reefs have formed recurrently in the Phanerozoic and occupied a central place in the development of Earth's complex interactions; as such, reefs are essentially a microcosm of the geobiological system. The long-term waxing and waning of reefs was governed not only by the evolution of organisms themselves, but also by cyclical marine conditions (e.g., calcitic sea vs. aragonitic sea; greenhouse vs. icehouse; oligotrophy vs. eutrophy; and carbonate saturation states) that led to the replacement of dominant kinds of taxa. Viewed in perspective, Palaeozoic to Mesozoic reefs changed fundamentally, particularly during greenhouse periods, due to the shifts in marine environmental regimes and ensuing improvements. Metazoan reefs formed temporarily immediately after the earliest Cambrian biomineralization and subsequently became dominant after the Ordovician radiations, as a consequence of networked geobiological interrelationships that were triggered by the invasion of biota onto land. Major extinctions were also triggers for the subsequent (re)diversifications of preexisting, potential reef builders, not necessarily accompanied by new higher taxa, and for the replacement of dominant organisms, whether reef builders or not. Given that certain regimes persisted, progressive, internal modifications and improvements also accelerated in accordance with niche exploitations that are clearly evidenced by changes in the overall growth morphologies of reef builders. Reefs as a microcosm should be further deciphered in light of how both skeletal organisms and microbes mutually responded to ambient, changing habitat conditions, and how sequential contributors prevailed in turn under given conditions at various spatio-temporal scales. Such studies would elucidate the evolution of geobiological constituents and their interrelationships with the underlying background, and more importantly, irreversibly progressive changes in Earth history.