Since the public awareness for climate change has risen, increasing scientific effort has been made to find and develop alternative resources and production processes to reduce the dependency on petrol-based fuels and chemicals of our society. Among others, the biotechnological fuel production, as for example fermenting sugar-rich crops to ethanol, is one of the main strategies. For this purpose, various classical production systems like Escherichia coli or Saccharomyces cerevisiae are used and have been optimized via genetic modifications. Despite the progress made, this strategy competes for nutritional resources and agricultural land. To overcome this problem, various attempts were made for direct photosynthetic driven ethanol synthesis with different microalgal species including cyanobacteria. However, compared to existing platforms, the development of cyanobacteria as photoautotrophic cell factories has just started, and accordingly, the ethanol yield of established production systems is still unreached. This is mainly attributed to low ethanol tolerance levels of cyanobacteria and there is still potential for optimizing the cyanobacteria towards alternative gene expression systems. Meanwhile, several improvements were made by establishing new toolboxes for synthetic biology offering new possibilities for advanced genetic modifications of cyanobacteria. Here, current achievements and innovations of those new molecular tools are discussed.