We will discuss the new insights on the phase structure of lattice QCD with Wilson fermions which has emerged from the exact computation of spectrum of the Wilson Dirac operator at nonzero lattice spacing. In addition to the spontaneous breaking of chiral symmetry, new phase structures known as the Aoki phase and the Sharpe-Singleton scenario can dominate. The new phases arise due to the interplay between the continuum and the chiral limit in lattice QCD with Wilson fermions and are essential for the study of non perturbative QCD at physical values of the pion masses. In particular, we will explain a long standing puzzle between the phase structure observed in quenched and unquenched lattice simulations.