A complete Supervisory Control And Data Acquisition system for microalgae industrial facilities has been developed. The software integrate the acquisition of information about weather conditions and parameters of the reactors to operate at optimal conditions the microalgae rectors allowing its maximal performance. All the steps of the process are controlled such as the preparation of culture medium. The continuous/semi-continuous dilution of the reactors, the harvesting and including the processing steps. A modular system that allows to implement or modify the different components of the process has been used. The software has been demonstrated at industrial scale under real industrial conditions.