Cyanothece sp. ATCC 51142 is considered a microorganism with the potential to generate sustainable hydrogen in the future. However, few kinetic models are capable of simulating different phases of Cyanothece sp. ATCC 51142 from growth to hydrogen production. In the present study four models are constructed to simulate Cyanothece sp batch photoprocluction process. A dynamic optimisation method is used to determine parameters in the models It is found that although the piecewise models fit experimental data better, large deviation can be induced when they are used to simulate a process whose operating conditions are different from the current experiments. The modified models are eventually selected in the present study to simulate a two-stage continuous photoproduction process. The current simulation results show that a plug flow reactor (PFR) shows worse performance compared to a continuous stirred tank reactor (CSTR) in the current operating conditions since it lowers the total hydrogen production. The finding is that nitrate and oxygen concentration change along the direction of culture movement in PFR, and hydrogen is only generated in the zone where both of them are low. The reactor area thereby is not well utilised. Additionally, as hydrogen production rate is primarily influenced by biomass concentration, which increases initially and decreases eventually along the direction of culture movement, the overall hydrogen production rate in a PFR may be lower than that in a CSTR. Finally, in this study fed batch photoproduction processes are proposed containing only one photobioreactor based on the current simulation. (C) 2015 The Authors. Published by Elsevier Ltd.