In my dissertation, we focus on the wireless network coexistence problem with advanced physical-layer techniques. For the first part, we study the problem of Wireless Body Area Networks (WBAN)s coexisting with cross-technology interference (CTI). WBANs face the RF cross-technology interference (CTI) from non-protocol-compliant wireless devices. Werst experimentally characterize the adverse effect on BAN caused by the CTI sources. Then we formulate a joint routing and power control (JRPC) problem, which aims at minimizing energy consumption while satisfying node reachability and delay constraints. We reformulate our problem into a mixed integer linear programing problem (MILP) and then derive the optimal results. A practical JRPC protocol is then proposed. For the second part, we study the coexistence of heterogeneous multi-hop networks with wireless MIMO. We propose a new paradigm, called cooperative interference mitigation (CIM), which makes it possible for disparate networks to cooperatively mitigate the interference to/from each other to enhance everyone's performance. We establish two tractable models to characterize the CIM behaviors of both networks by using full IC (FIC) and receiver-side IC (RIC) only. We propose two bi-criteria optimization problems aiming at maximizing both networks' throughput, while cooperatively canceling the interference between them based on our two models. In the third and fourth parts, we study the coexistence problem with MIMO from a different point of view: the incentive of cooperation. We propose a novel two-round game framework, based on which we derive two networks' equilibrium strategies and the corresponding closed-form utilities. We then extend our game-theoretical analysis to a general multi-hop case, specifically the coexistence problem between primary network and multi-hop secondary network in the cognitive radio networks domain. In the final part, we study the benefits brought by reconfigurable antennas (RA). We systematically exploit the pattern diversity and fast reconfigurability of RAs to enhance the throughput of MWNs. Werst propose a novel link-layer model that captures the dynamic relations between antenna pattern, link coverage and interference. Based on our model, a throughput optimization framework is proposed by jointly considering pattern selection and link scheduling, which is formulated as a mixed integer non-linear programming problem.