In the model green alga Chlamydomonas reinhardtii, a carbon concentrating mechanism (CCM) is induced under low CO2 in the light and comprises: active inorganic carbon transport components, carbonic anhydrases and aggregation of Rubisco in the chloroplast pyrenoid. Previous studies have focused predominantly on asynchronous cultures of cells grown under low versus high CO2. Here, we have investigated the dynamics of CCM activation in synchronised cells grown in dark/light cycles, as compared to induction under low CO2. The specific focus was to undertake detailed time course experiments comparing physiology and gene expression during the dark to light transition. Firstly, the CCM could be fully induced one hour before dawn, as measured by the K0.5 for inorganic carbon (Ci). This occurred in advance of maximum gene transcription and protein accumulation and contrasted with the co-ordinated induction observed under low CO2. Between two hours and one hour before dawn, the proportion of Rubisco and the thylakoid lumen carbonic anhydrase, CAH3, in the pyrenoid rose substantially, coincident with increased CCM activity. Thus, other mechanisms are likely to activate the CCM before dawn, independent of gene transcription of known CCM components. Furthermore, this study highlights the value of using synchronised cells during the dark to light transition as an alternative means of investigating CCM induction.