Background Genetic engineering of microorganisms typically redirects native metabolism towards desirable products, which thereby represent new metabolic sinks. The is a limited information regarding the extent on how these modifications impact the evolved mechanisms of metabolism. It was previously shown that a heterologous sucrose sink in cyanobacteria improves multiple photosynthetic parameters. An efficient method to analyze large metabolic networks is constraint-based modeling, which imposes stoichiometric constraints on the metabolic reactions and analyzes the possible flux solutions at steady state. Flux balance analysis (FBA) is a common approach to calculate, under given constraints, the intracellular flux distributions within the stoichiometric network, by optimizing an objective function. Besides photoautotrophic conditions, the model cyanobacterium Synechocystis sp. PCC 6803 is able to grow under mixotrophic conditions, a promising cultivation strategy due to the enhanced biomass and chemical yield, as compared to the former. To date, the contribution of heterologous carbon sink, as well as the extent to which specific reactions can carry a flux under photoautotrophic and mixotrophic growth is not known. Aim We aim to provide insight into the size and shape of the solution space, thereby shed light on the phenotypic plasticity of Synechocystis. More specifically, we will get insights into the network robustness, which may facilitate metabolic engineering strategies towards enhanced production of end-products. Methods We will apply flux sampling analysis, which computes the flux ranges for each reaction, as well as generates an unbiased probability of the steady-state flux distributions. Hence, flux sampling analysis is a powerful method for analyzing both metabolic shifts following the induction of a heterologous carbon sink, and the metabolic capabilities under different growth conditions.