We are investigating the Evolution of the Complex Regulatory Networks by using Systems Approach. When organism is challenged by different environmental stimuli, architecture of the Gene Regulatory Networks can change rapidly and efficiently to increase fitness in the new environment. This is one of the earliest events in adaptive evolution that creates Biological Complexity and Diversity. For tracking the evolution of GRN, we start with the Halobacterium Regulatory network that involves many layers of regulation including Eukaryotic type general transcription factors and bacterial type regulators. We construct library of rewired TF networks by introducing variations at different levels of the network such as DNA binding sites, protein interaction interfaces or promoter specificites. We challange these networks with different environmental perturbations and screen for improved fitness to identify optimal network solutions.