We investigate the Berry phase of adiabatic quantum evolution in the atom–molecule conversion system that is governed by a nonlinear Schrödinger equation. We find that the Berry phase consists of two parts: the usual Berry connection term and a novel term from the nonlinearity brought forth by the atom–molecule coupling. The total geometric phase can be still viewed as the flux of the magnetic field of a monopole through the surface enclosed by a closed path in parameter space. The charge of the monopole, however, is found to be one third of the elementary charge of the usual quantized monopole. We also derive the classical Hannay angle of a geometric nature associated with the adiabatic evolution. It exactly equals minus Berry phase, indicating a novel connection between Berry phase and Hannay angle in contrast to the usual derivative form