Aeroelastic design of joined-wing configurations is yet a relatively unexplored topic which poses several difficulties. Due to the overconstrained nature of the system combined with structural geometric nonlinearities, the behavior of Joined Wings is often counterintuitive and presents challenges not seen in standard layouts. In particular, instability observed on detailed aircraft models but never thoroughly investigated, is here studied with the aid of a theoretical/computational framework. Snap-type of instabilities are shown for both pure structural and aeroelastic cases. The concept of snap-divergence is introduced to clearly identify the true aeroelastic instability, as opposed to the usual aeroelastic divergence evaluated through eigenvalue approach. Multi-stable regions and isola-type of bifurcations are possible characterizations of the nonlinear response of Joined Wings, and may lead to branch-jumping phenomena well below nominal critical load condition. Within this picture, sensitivity to (unavoidable) manufacturing defects could have potential catastrophic effects. The phenomena studied in this work suggest that the design process for Joined Wings needs to be revisited and should focus, when instability is concerned, on nonlinear post-critical analysis since linear methods may provide wrong trend indications and also hide potentially catastrophical situations. Dynamic aeroelastic analyses are also performed. Flutter occurrence is critically analyzed with frequency and time-domain capabilities. Sensitivity to different-fidelity aeroelastic modeling (fluid-structure interface algorithm, aerodynamic solvers) is assessed showing that, for some configurations, wake modeling (rigid versus free) has a strong impact on the results. Post-flutter regimes are also explored. Limit cycle oscillations are observed, followed, in some cases, by flip bifurcations (period doubling) and loss of periodicity of the solution. Aeroelastic analyses are then carried out on a realistic PrantlPlane to understand effects induced by freeplay of mobile surfaces. Conclusive work is also performed to study the interaction between rigid body and elastic modes, assessing the occurrence of bodyfreedom flutter.