Casein Kinase 2 (CK2) is an evolutionarily conserved kinase protein that phosphorylates a plethora of cellular target protein involved in processes including DNA repair, cell cycle control, and circadian rhythms. CK2 is functionally conserved across all eukaryotes, although the substrate proteins identified in targeted experiments on a diverse range of complex tissues are often different. A growing interest exists to identify conserved, core signalling principles essential to eukaryotic life. To efficiently study generic roles of CK2 in the cellular circadian clock, we used a minimal eukaryotic model organism (Ostreococcus tauri). Overexpression of CK2 leads to a slow circadian rhythm, verifying functional conservation of CK2 in cellular timekeeping. CK2 activity contributes more strongly to the clock around dusk than around dawn, and analysis of the phospho-proteome at this time revealed a strong overrepresentation of potential CK2 sites. Large changes to the phospho-proteome are reported here upon overexpression of CK2, identifying a set of CK2-responsive phospho-sites. To identify more CK2-specific phosphorylation events, the phospho-proteome of cells treated with CK2 inhibitor were analysed and compared to the overexpression lines. We thus report a full inventory of the CK2-responsive phospho-proteome to inform studies into CK2 activity in the circadian clock of more complex tissues, as science moves to understand and modulate cellular circadian rhythms to help us negate the negative effects of shiftwork or cross-continental travel.