Blue light regulates processes such as the development of plants and fungi and the behaviour of microbes. Two types of blue-light receptor flavoprotein have been identified: cryptochromes, which have partial similarity to photolyases, and phototropins, which are photoregulated protein kinases. The former have also been found in animals with evidence of essential roles in circadian rhythms. Euglena gracilis, a unicellular flagellate, abruptly changes its swimming direction after a sudden increase or decrease in incident blue light intensity, that is, step-up or step-down photophobic responses, resulting in photoavoidance or photoaccumulation, respectively. Although these photobehaviours of Euglena have been studied for a century, the photoreceptor molecules mediating them have remained unknown. Here we report the discovery and biochemical characterization of a new type of blue-light receptor flavoprotein, photoactivated adenylyl cyclase, in the photoreceptor organelle of Euglena gracilis, with molecular genetic evidence that it mediates the step-up photophobic response.