Modal-based, nonlinear Moving Horizon Estimation (MHE) and Model Predictive Control (MPC) strategies for highly flexible aeroelastic systems are presented. The aeroelastic model is built from a 1D intrinsic (based on strains and velocities) description of geometrically-nonlinear beams and an unsteady Vortex Lattice aerodynamic model. Construction of a nonlinear modalbased reduced order model of the aeroelastic system, employing a state-space realisation of the linearised aerodynamics around an arbitrary equilibrium point, allows us to capture the main nonlinear geometrical couplings at a very low computational cost. Embedding this model in both MHE and MPC strategies, which solve the system's continuous-time adjoints efficiently to compute sensitivities, lays the foundations for real-time estimation and control of highly flexible aeroelastic systems.