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In the unicellular, spherical cyanobacterium Synechocystis sp. PCC6803, unidirectional light can be focused to the rear side of the cell as a sharp image which controls the activity of the type IV pilus (T4P) motility apparatus which is activated for negative phototaxis or inhibited for positive phototaxis. Three photoreceptors are implicated in the regulation of phototaxis, including the blue/green light cyanobacteriochrome (CBCR) PixJ, the UV-A light CBCR UirS and the blue light sensor PixD. To determine the mechanism of UV-A light induced phototaxis, the spatial localisation of UirS and the downstream response regulator LsiR were investigated with fluorescent protein tags (eYFP) by confocal microscopy. UirS is not evenly distributed on the plasma membrane which indicates it cannot accurately sense UV-A light from various directions independently. The distribution pattern of LsiR-eYFP with and without the T4P extension ATPase motor PilB1 are significantly different, which suggests that LsiR interacts with PilB1 for localised T4P regulation. To determine whether multiple photoreceptors could contribute to directional light sensing, knockouts for PixJ, UirS and PixD were constructed in combinations. However, none of the photoreceptors are essential for directional light sensing because all of the mutants still retain directionality. Surprisingly, a dramatic reduction of directionality in single cell motility assays was observed with treatment of an inhibitor for plastoquinone (PQ) pool oxidation on photosynthetic electron transport chain (ETC) that demonstrates that the oxidized PQ pool is the essential directional light sensor. Additionally, a violet photoreceptor CikA which was previously reported in Synechococcus elongatus to rest the circadian clock directly interacts with PQ. Knockout of the Synechocystis CikA homolog led to a significant reduction of directionality which suggests that CikA is involved in modulation of localised T4P regulation for phototaxis.