The prediction of the weather at subseasonal-to-seasonal (S2S) timescales is dependent on both initial and boundary conditions. An open question is how to best initialize a relatively small-sized ensemble of numerical model integrations to produce reliable forecasts at these timescales. Reliability in this case means that the statistical properties of the ensemble forecast are consistent with the actual uncertainties about the future state of the geophysical system under investigation. In the present work, a method is introduced to construct initial conditions that produce reliable ensemble forecasts by projecting onto the eigenfunctions of the Koopman or the Perron-Frobenius operators, which describe the time-evolution of observables and probability distributions of the system dynamics, respectively. These eigenfunctions can be approximated from data by using the Dynamic Mode Decomposition (DMD) algorithm. The effectiveness of this approach is illustrated in the framework of a low-order ocean-atmosphere model exhibiting multiple characteristic timescales, and is compared to other ensemble initialization methods based on the Empirical Orthogonal Functions (EOFs) of the model trajectory and on the backward and covariant Lyapunov vectors of the model dynamics. Projecting initial conditions onto a subset of the Koopman or Perron-Frobenius eigenfunctions that are characterized by time scales with fast-decaying oscillations is found to produce highly reliable forecasts at all lead times investigated, ranging from one week to two months. Reliable forecasts are also obtained with the adjoint covariant Lyapunov vectors, which are the eigenfunctions of the Koopman operator in the tangent space. The advantages of these different methods are discussed.