We investigate the effect of the anisotropy of a harmonic trap on the behaviour of a fast rotating Bose-Einstein condensate. This is done in the framework of the 2D Gross-Pitaevskii equation and requires a symplectic reduction of the quadratic form defining the energy. This reduction allows us to simplify the energy on a Bargmann space and study the asymptotics of large rotational velocity. We characterize two regimes of velocity and anisotropy; in the first one where the behaviour is similar to the isotropic case, we construct an upper bound: a hexagonal Abrikosov lattice of vortices, with an inverted parabola profile. The second regime deals with very large velocities, a case in which we prove that the ground state does not display vortices in the bulk, with a 1D limiting problem. In that case, we show that the coarse grained atomic density behaves like an inverted parabola with large radius in the deconfined direction but keeps a fixed profile given by a Gaussian in the other direction. The features of this second regime appear as new phenomena.