In systems biology, one of the ultimate goals is to engineer unnatural organic molecules that function in living systems so as to investigate natural biological phenomena and further redesign new biological systems for useful purposes. In control engineering, the overall aim is to synthesize controllers which can achieve desired performance. The notion of feedback, which is the core of control engineering, is now a central recurring theme in the design of biological regulatory networks. In fact, feedback is so prevalent in biological systems that it can be found at all levels of the organization, from molecular and cellular levels to organism and ecological. It is unreasonable to overstate the importance of feedback as a strategy for the maintenance and evolution of life. Instead, it makes more practical sense to expect that ideas from control theory will lead to new understanding of the underlying biological processes, and further facilitate potential applications in systems biology and synthetic biology. On the other hand, the complexity of biological networks poses many challenges for scientists and engineers. In particular, the biological systems have apparently become dependent on the complex infrastructure of the networks to such an extent that it is difficult to analyze and control these networks thoroughly with our current capabilities. As such, there is an urgent need to research into modelling, analyzing and controlling biological networks with available systems and control theory. Although many fundamental questions have been addressed with hope to understand network structures and dynamic properties, some major problems from systems viewpoint have not been fully investigated, such as issues concerning switching, oscillating, stability, sensitivity, robustness, synchronization, design principle, and nonlinear control for biological networks. This special issue aims to bring together the latest advances in analysis and control of biological networks, which comprise the following topics: a tutorial of feedback mechanism in biological network models, stability region of photosynthetic carbon metabolism, stability analysis on genetic regulatory networks, robust stability analysis of switching gene regulatory networks , robustness analysis on stochastic immune systems, bifurcation analysis of biochemical signaling pathways, adaption model of molecular networks, synchronization in networks of genetic oscillators, bio-entity network for analysis of protein-protein interaction networks, and a simulator for intracellular transport analysis. We hope that readers will benefit from reading the articles of this issue. Finally, the guest editorswish to thank all the authors and the reviewers for their contributions to this special issue.