In this paper, we propose a methodology to design chaos-based communication systems, which exploits the topological structure of 3-D chaotic attractors. The first step consists in defining a proper partition of a Poincaré section of the attractor and the subsequent encoding of the chaotic trajectories. Then, the evolution mechanism of the chaotic attractor, according to the dynamical restrictions imposed by the chaotic flow, is represented by a state diagram, where each state represents a region of the Poincaré section or a branch in the template of the chaotic attractor. The state transitions are associated with segments of chaotic trajectories that connect the corresponding regions of the Poincaré section. The chaotic signals are transmitted over both additive white Gaussian noise and Rayleigh flat fading channels, and a trellis structure derived from the state diagram is used at the decoder to estimate the transmitted information sequence. Finally, the bit error rate performance of the system is analyzed.