The manned aircraft missions are highly risky for deep penetration into enemy territory, because the effectiveness and density of modern air defense systems and the high vulnerability of aircraft systems. In view of this situation, advanced tactical UAV are considered as suitable to take over such missions. In this work, a mathematical model describes the aircraft dynamics in three dimensions was presented. The linearized mathematical model of the longitudinal and lateral channels is obtained by using advanced aircraft analysis program. In addition, the solution of the five-degree of freedom nonlinear equations of motion was solved using MATLAB. Also, modeling and identification for the servo motor is achieved by using RLS algorithm. In this work, two approaches were presented in the design and analysis of the proposed aircraft autopilot: (i) the off-line learning of the parameters of PID controller using GAs; (ii) the on-line learning by using IAC. An alternative modified GA structure is achieved to improve the GA performance. Finally, the analysis and design of the overall control and guidance system was achieved for different flight conditions, to increase system stability.