Much of industrially relevant phenotypes in biological systems are complex and involve multiple genes and mechanisms. The identities of these genetic determinants are generally not known, making the rational engineering of strains for these complex phenotypes challenging. If the desired trait can be coupled with growth, in vitro adaptive evolution can be used to improve the desired phenotype. This process is accomplished by applying a selective pressure so that beneficial mutants (mutants with increased fitness) can be obtained through the process of natural selection. The adaptive landscape is used to describe the collection of relative fitness effects of each genotype under a specific condition. Detailed molecular characterization of adaptive mutants isolated from in vitro adaptive evolution experiments provides insights into the adaptive landscape for the phenotype of interest. Characterization of the adaptive landscape will significantly enhance our knowledge on the important parameters underlying complex phenotypes needed for the rational engineering of strains. However, traditional laboratory evolution methods have several limitations, such as the lack of rational schemes for the isolation of adaptive mutants and the ramp-up in selective pressure and the inability to recombine synergistic mutations for faster rate of evolutionary engineering. Our lab is focused on the development of more effective and efficient adaptive evolution methods to address these limitations for both strain engineering and for the fundamental understanding of evolutionary processes in microbial systems.