Abstract. In Part I of this study Whitehouse et al. (2005) performed a diagnostic analysis of a simplied model of the Martian atmosphere, in which topography was absent and in which heating was modelled as Newtonian relaxation towards a zonally symmetric equilibrium temperature field. There we derived a reduced-order approximation to the vertical and the horizonal structure of the baroclinically unstable Martian atmosphere, retaining only the barotropic mode and the leading order baroclinic modes. Our objectives in Part II of the study are to incorporate these approximations into a Proper Orthogonal Decomposition-Galerkin expansion of the spherical quasi-geostrophic model in order to derive hierarchies of nonlinear ordinary differential equations for the time-varying coefficients of the spatial structures. Two different vertical truncations are considered, as well as three different norms and 3 different Galerkin truncations. We investigate each in turn, using tools from bifurcation theory, to determine which of the systems most closely resembles the data for which the original diagnostics were performed.