Within the blue biotechnology, the cultivation of microalgae has an important role. Aimed is the production of valuable bio products, including biofuels. Microalgae can be cultivated in open raceway ponds or in different types of photobioreactors (PBRs). Besides their higher investment costs, PBRs are gaining more importance due to the possibilities they offer for controlling the production parameters like, light, pH, Nutrients, CO 2 supply, etc. This study presents the influence of temperature control on the operating cost of a culture in a flat-panel airlift photobioreactor, based on a simulation model. The data used are those of a coastal range in Cyprus, at Zygi, with mild climate, requiring heating in Winter and cooling in the Summer. Microalgae grow optimally between 20°C and 24°C, but choosing the right set temperatures for Winter and Summer plays an important role in the economy of the system. The most energy saving option seems to be that of a stepwise set-temperature control, with a temperature varying in steps between 19 and 24°C that are considered to be economic acceptable minimum and maximum values. For the estimation of the yearly fuel consumption of the PBR a new term, the Burner ON Ratio was introduced.