Summary: There are numerous examples of long-lived, surface-intensified anticyclones over submarine depressions and troughs in the ocean. These often co-exist with a large-scale cyclonic circulation. The latter is predicted by existing barotropic theory but the anticyclone is not. We extend one such theory, which minimizes enstrophy while conserving energy, to two fluid layers. This yields a bottom-intensified flow with cyclonic circulation over a depression. The solution is steady, an enstrophy minimum and stable. When the Lagrange multiplier, \(\lambda\), is near zero, the total potential vorticity (PV) becomes homogenized, in both layers. For positive \(\lambda\), the surface PV is anticyclonic and strongest at intermediate energies. In quasi-geostrophic numerical simulations with a random initial perturbation PV, the bottom-intensified cyclonic flow always emerges. Vortices evolve independently in the layers and vortex mergers are asymmetric over the depression; cyclones are preferentially strained out at depth while only anticyclones merge at the surface. Both asymmetries are linked to the topographic flow. The deep cyclones feed the bottom-intensified cyclonic circulation while the asymmetry at the surface is only apparent after that circulation has spun up. The result of the surface merger asymmetry is often a lone anticyclone above the depression. This occurs primarily at intermediate energies, when the surface PV predicted by the theory is strongest. Similar results obtain in a full complexity ocean model but with a more pronounced asymmetry in surface vortex mergers and, with bottom friction, significant bottom flow beneath the central anticyclone.