Life on earth is strongly affected by the day-night cycle, also known as the diurnal cycle. Due to its importance in survival, many organisms have developed an internal time keeping mechanism that goes by the name of circadian rhythm. Light plays a vital role for photosynthetic cyanobacteria and changes in the light pattern result in adaptive changes in the underlying biological processes at cellular level. Processes under circadian control are able to maintain their rhythm even under changes in the diurnal cycle, and it is important to isolate these processes from those whose rhythms are strongly affected by light. As the only known prokaryotic organism to have a robust circadian clock mechanism, cyanobacteria provide us with a unique opportunity to unveil the complex changes, especially changes in the process rhythms resulting from perturbation of the diurnal cycle. In this paper, we have identified the circadian controlled genes from those that are strongly influenced by light using a pair of genome wide study utilizing microarrays. A transcription model with an associated regulatory network is proposed.