In order to minimize the global dependency of fossil fuels, researchers have visionised the prospect of utilizing photosynthetic cyanobacteria for converting atmospheric CO2into carbon neutral biofuels. Isobutanol has been identified as one of the most potent biofules due to its high energy content and is compatible to existing combustion engines. The advent of increasing number of genetic tools has during the last decades made it possible to introduce the synthetic 2-keto acid pathway for heterologous isobutanol production in cyanobacteria. This study assessed the performance of four recently engineered Synechocystis strains in their long-term isobutanol production. By pH adjusting the cultures and regular media replenishment, continuous isobutanol production was observed with gas chromatography for 60 days. The results identified strains HX29 and HX42 as having superior performance compared to previous isobutanol producing cyanobacteria. After almost 60 days of continuous production, the maximum cumulative titers were 1.25 g/L and 1.19 g/L for HX29 respectively HX42. However, the performance varied significantly between the replicates of HX42 whilst HX29 gave more consistent results. Genetic instability and isobutanol stress responses are discussed to be the underlying reasons for the variation in performance between the strains. Furthermore, this study also introduced two of Synechocystis native 2-keto acid pathway genes as a first step of allowing future studies to overexpress the whole pathway. The relatively weak, metal inducible, pPetE-promoter was shown to be the best candidate for driving expression of the native 2-keto acid pathway. This strain could serve as a foundation for future strains containing the whole native 2-keto acid pathway.