We establish quantum thermodynamics for open quantum systems weakly coupled to their reservoirs when the system exhibits degeneracies. The first and second law of thermodynamics are derived, as well as a finite-time fluctuation theorem for mechanical work and energy and matter currents. Using a double quantum dot junction model, local eigenbasis coherences are shown to play a crucial role on thermodynamics and on the electron counting statistics. ; Comment: 36 pages, 7 figures