The common view that circadian rhythms evolved as an adaptation to the exogenous daily cycle is questioned regarding early eukaryotic unicellulars. An alternative explanation of their origin is presented: circadian ‐ and other endogenous ‐ rhythms made available a temporal coordination mechanism to those intracellular symbioses which developed into eukaryotic cells. For the functioning of such associations a synchronization between host cells and endosymbionts has to be considered essential. It may have been achieved by the coupling of cellular activities to endogenous rhythms.