During the last decade, the genomics revolution has created powerful instruments for genetic manipulation of living organisms. In addition, new biotechnological tools allow to modify organisms in order to perform specific tasks. In particular, synthetic biology is an emerging trans-disciplinary field that uses engineering principles to design and assemble novel biological components. For example, within the area of industrial microbiology, synthetic biology has contributed to build from scratch or re-engineer new microorganisms or chemical compounds. However, all these scientific and biotechnological innovations present a substantial challenge also for the law and especially for intellectual property rights. Considering this multifaceted scenario, this chapter discuss the current challenges and opportunities at the intersection of synthetic biology, microbiology and intellectual property also proposing alternative form of protection for genetically engineered works created by using synthetic biology.