Biomimetic flapping-wing vehicles have attracted recent interest because of their numerous potential military and civilian applications. In this dissertation is described the design of a multi-agent adaptive controller for such a vehicle. This controller is responsible for estimating the vehicle pose (position and orientation) and then generating four parameters needed for split-cycle control of wing movements to correct pose errors. These parameters are produced via a subsumption architecture rule base. The control strategy is fault tolerant. Using an online learning process, an agent continuously monitors the vehicle's behavior and initiates diagnostics if the behavior has degraded. This agent can then autonomously adapt the rule base if necessary. Each rule base is constructed using a combination of extrinsic and intrinsic evolution. Details of the vehicle, the multi-agent system architecture, agent task scheduling, rule base design, and vehicle control are provided.