Synechocystis sp. PCC 6803 is a unicellular motile cyanobacterium that shows positive and negative phototaxis on agar plates under lateral illumination. Recent studies on the molecular mechanisms of the phototactic motility of Synechocystis have revealed that a number of genes are responsible for its pilus-dependent motility and phototaxis. Here we describe what is known about these genes. We also discuss the novel spectral properties of the phytochrome-like photoreceptor PixJ1 in Synechocystis, that is essential for positive phototaxis and which has revealed the existence of a new group of chromophore-binding proteins in cyanobacteria.