The paper presents a theory for flight-dynamic analysis of highly flexible flying-wing configurations. The analysis takes into account large aircraft motion coupled with geometrically nonlinear structural deformation subject only to a restriction to small strain. A large motion aerodynamic loads model is integrated into the analysis. The analysis can be used for complete aircraft analysis including trim, stability analysis linearized about the trimmed-state, and nonlinear simulation. Results are generated for a typical high-aspect-ratio "flying-wing" configuration. The results indicate that the aircraft undergoes large deformation during trim. The flight-dynamic characteristics of the deformed aircraft are completely different as compared with a rigid aircraft. When the example aircraft is loaded sufficiently, the pair of complex-conjugate short-period roots merges to become two real roots, and the phugoid mode goes unstable. Furthermore, nonlinear flight simulation of the aircraft indicates that the phugoid instability leads to catastrophic consequences.