Under the current global energy crisis the interests in developing a third generation of biofuels produced from non-food feedstock such as microalgae and cyanobacteria have clearly increased. Hydrodynamic stress, always present in cultivation process of these microorganisms, is an essential factor to ensure mixing inside bioreactors; however the importance of its intensity is usually ignored by applying a random agitation (energy consumption) which is unnecessarily overestimated. In this work, two types of agitation, stirring in agitated photobioreactors (APBR) and bubbling air in draft tube airlift photobioreactors (DPBR), are applied to study the effects of hydrodynamic stress on the growth and pigment content evolution of the cyanobacteria Synechocystis sp. PCC 6803, a self-propelled microorganism. The range of applied shear stress was between 0 and 400 mPa. Similar results are obtained for both agitation mechanisms, indicating that the effects of shear stress are limited to the breakdown of the cell colonies; once they are broken down any further increase in shear stress has no significant effect on their growth rate. Moreover, the variation in pigments concentration appeared to be linear with the cellular concentration and independent from shear intensity.