Microcystin-LR (MC-LR), an inert electrochemical species, is difficult to be detected by a simple and direct electrochemical method. In the present work, a novel photoelectrochemical sensor is developed on highly ordered and vertically aligned TiO(2) nanotubes (TiO(2) NTs) with convenient surface modification of molecularly imprinted polymer (MIP) (denoted as MIP@TiO(2) NTs) for highly sensitive and selective determination of MC-LR in solutions. Molecularly imprinted polypyrrole (PPy) of MC-LR is chosen as the recognition element. The designed MIP@TiO(2) NTs photoelectrochemical sensor presents excellent applicability in MC-LR determination, with linear range from 0.5 to 100 μg L(-1) and limit of detection of 0.1 μg L(-1). Moreover, the sensor exhibits outstanding selectivity while used in coexisting systems containing 2,4-dichorophenoxyacetic acid, atrazine, paraquat, or monosultap with high concentration, 100 times that of MC-LR. The sensor presents good photoelectric conversion efficiency and detection sensitivity, as well as broad linear detection range, mainly because of the high specific surface area and photoelectric activity of TiO(2) NTs and the π bond delocalized electron system of PPy that promotes the separation of electron-holes. The prominent selectivity is from the MIP by forming multiple hydrogen bonds between PPy and MC-LR. Mechanisms for photoelectrochemical analysis and selective recognition are also discussed.